1
|
Wenne R. Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:1089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
Collapse
Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| |
Collapse
|
2
|
Sundaray JK, Dixit S, Rather A, Rasal KD, Sahoo L. Aquaculture omics: An update on the current status of research and data analysis. Mar Genomics 2022; 64:100967. [PMID: 35779450 DOI: 10.1016/j.margen.2022.100967] [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: 06/17/2021] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.
Collapse
Affiliation(s)
- Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan University (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Ashraf Rather
- Division of Fish Genetics and Biotechnology, College of Fisheries, Sher-e- Kashmir University of Agricultural Science and Technology, Rangil-Ganderbal 190006, Jammu and Kashmir, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400 061, Maharastra, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
| |
Collapse
|
3
|
Momeni J, Parejo M, Nielsen RO, Langa J, Montes I, Papoutsis L, Farajzadeh L, Bendixen C, Căuia E, Charrière JD, Coffey MF, Costa C, Dall'Olio R, De la Rúa P, Drazic MM, Filipi J, Galea T, Golubovski M, Gregorc A, Grigoryan K, Hatjina F, Ilyasov R, Ivanova E, Janashia I, Kandemir I, Karatasou A, Kekecoglu M, Kezic N, Matray ES, Mifsud D, Moosbeckhofer R, Nikolenko AG, Papachristoforou A, Petrov P, Pinto MA, Poskryakov AV, Sharipov AY, Siceanu A, Soysal MI, Uzunov A, Zammit-Mangion M, Vingborg R, Bouga M, Kryger P, Meixner MD, Estonba A. Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs. BMC Genomics 2021; 22:101. [PMID: 33535965 PMCID: PMC7860026 DOI: 10.1186/s12864-021-07379-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. RESULTS Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. CONCLUSIONS The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.
Collapse
Affiliation(s)
- Jamal Momeni
- Eurofins Genomics Europe Genotyping A/S (EFEG), (Former GenoSkan A/S), Aarhus, Denmark.
| | - Melanie Parejo
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain.,Swiss Bee Research Center, Agroscope, Bern, Switzerland
| | - Rasmus O Nielsen
- Eurofins Genomics Europe Genotyping A/S (EFEG), (Former GenoSkan A/S), Aarhus, Denmark
| | - Jorge Langa
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | - Iratxe Montes
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | - Laetitia Papoutsis
- Laboratory of Agricultural Zoology and Entomology, Agricultural University of Athens, Athens, Greece
| | - Leila Farajzadeh
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Christian Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eliza Căuia
- Institutul de Cercetare Dezvoltare pentru Apicultura SA, Bucharest, Romania
| | | | | | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | | | | | | | - Janja Filipi
- Department of Ecology, Agronomy and Aquaculture, University of Zadar, Zadar, Croatia
| | | | | | - Ales Gregorc
- Faculty of Agriculture and Life Sciences, University of Maribor, Maribor, Slovenia
| | | | - Fani Hatjina
- Department of Apiculture, Agricultural Organization 'DEMETER', Thessaloniki, Greece
| | - Rustem Ilyasov
- Division of Life Sciences, Major of Biological Sciences, and Convergence Research Center for Insect Vectors, Incheon National University, Incheon, Korea.,Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | | | | | | | | | | | | | | | - David Mifsud
- Division of Rural Sciences and Food Systems, Institute of Earth Systems, University of Malta, Msida, Malta
| | - Rudolf Moosbeckhofer
- Österreichische Agentur für Gesundheit und Ernährungssicherheit GmbH, Wien, Austria
| | - Alexei G Nikolenko
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | | | - Plamen Petrov
- Agricultural University of Plovdiv, Plovdiv, Bulgaria
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Aleksandr V Poskryakov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | | | - Adrian Siceanu
- Institutul de Cercetare Dezvoltare pentru Apicultura SA, Bucharest, Romania
| | | | - Aleksandar Uzunov
- Landesbetrieb Landwirtschaft Hessen, Bee Institute Kirchhain, Kirchhain, Germany.,Faculty of Agricultural Sciences and Food, University Ss. Cyril and Methodius, Skopje, Republic of Macedonia
| | | | - Rikke Vingborg
- Eurofins Genomics Europe Genotyping A/S (EFEG), (Former GenoSkan A/S), Aarhus, Denmark
| | - Maria Bouga
- Laboratory of Agricultural Zoology and Entomology, Agricultural University of Athens, Athens, Greece
| | - Per Kryger
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Marina D Meixner
- Landesbetrieb Landwirtschaft Hessen, Bee Institute Kirchhain, Kirchhain, Germany
| | - Andone Estonba
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain.
| |
Collapse
|
4
|
Langa J, Estonba A, Conklin D. EXFI: Exon and splice graph prediction without a reference genome. Ecol Evol 2020; 10:8880-8893. [PMID: 32884664 PMCID: PMC7452765 DOI: 10.1002/ece3.6587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 11/19/2022] Open
Abstract
For population genetic studies in nonmodel organisms, it is important to use every single source of genomic information. This paper presents EXFI, a Python pipeline that predicts the splice graph and exon sequences using an assembled transcriptome and raw whole-genome sequencing reads. The main algorithm uses Bloom filters to remove reads that are not part of the transcriptome, to predict the intron-exon boundaries, to then proceed to call exons from the assembly, and to generate the underlying splice graph. The results are returned in GFA1 format, which encodes both the predicted exon sequences and how they are connected to form transcripts. EXFI is written in Python, tested on Linux platforms, and the source code is available under the MIT License at https://github.com/jlanga/exfi.
Collapse
Affiliation(s)
- Jorge Langa
- Department of Genetics, Physical Anthropology and Animal PhysiologyFaculty of Science and TechnologyUniversity of the Basque CountryLeioaSpain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal PhysiologyFaculty of Science and TechnologyUniversity of the Basque CountryLeioaSpain
| | - Darrell Conklin
- Department of Computer Science and Artificial Intelligence, Faculty of Computer ScienceUniversity of the Basque Country UPV/EHUSan SebastiánSpain
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| |
Collapse
|
5
|
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PLoS One 2019; 14:e0213992. [PMID: 30889192 PMCID: PMC6424483 DOI: 10.1371/journal.pone.0213992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/05/2019] [Indexed: 11/19/2022] Open
Abstract
Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (FST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.
Collapse
|
6
|
Liu L, Wang Y, He P, Li P, Lee J, Soltis DE, Fu C. Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. BMC Genomics 2018; 19:235. [PMID: 29618324 PMCID: PMC5885378 DOI: 10.1186/s12864-018-4633-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4633-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yuewen Wang
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Peizi He
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, 34134, South Korea
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
7
|
Jacobs A, De Noia M, Praebel K, Kanstad-Hanssen Ø, Paterno M, Jackson D, McGinnity P, Sturm A, Elmer KR, Llewellyn MS. Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach. Sci Rep 2018; 8:1203. [PMID: 29352185 PMCID: PMC5775277 DOI: 10.1038/s41598-018-19323-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/17/2017] [Indexed: 12/13/2022] Open
Abstract
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
Collapse
Affiliation(s)
- A Jacobs
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - M De Noia
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - K Praebel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - M Paterno
- Department of Biology, University of Padova, Padova, Italy
| | | | - P McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - A Sturm
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - K R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - M S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
8
|
Bich Vo TT. Identification and analysis of snps in population of Vietnamese catfish (pangasianodon hypophthalmus), using next generation sequencing and snp validation. ACTA ACUST UNITED AC 2018. [DOI: 10.15406/mojcrr.2018.01.00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
9
|
Adaptation Without Boundaries: Population Genomics in Marine Systems. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
10
|
Montes I, Laconcha U, Iriondo M, Manzano C, Arrizabalaga H, Estonba A. Reduced Single Nucleotide Polymorphism Panels for Assigning Atlantic Albacore and Bay of Biscay Anchovy Individuals to Their Geographic Origin: Toward Sustainable Fishery Management. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4351-4358. [PMID: 28489943 DOI: 10.1021/acs.jafc.7b00619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is an increasing trend upon adding a detailed description of the origin of seafood products driven by a general interest in the implementation of sustainable fishery management plans for the conservation of marine ecosystems. North Atlantic albacore ("Bonito del Norte con Eusko Label") and Bay of Biscay anchovy ("Anchoa del Cantábrico") are two commercially important fish populations with high economical value and vulnerable to commercial fraud. This fact, together with the overexploited situation of these two populations, makes it necessary to develop a tool to identify individual origin and to detect commercial fraud. In the present study, we have developed and validated a traceability tool consisting of reduced panels of gene-associated single nucleotide polymorphisms (SNPs) suitable for assigning individuals of two species to their origin with unprecedented accuracy levels. Only 48 SNPs are necessary to assign 81.1% albacore and 93.4% anchovy individuals with 100% accuracy to their geographic origin. The total accuracy of the results demonstrates how gene-associated SNPs can revolutionize food traceability. Gene-associated SNP panels are not of mere commercial interest, but they also can result in a positive impact on sustainability of marine ecosystems through conservation of fish populations through establishing a more effective and sustainable fishery management framework and contributing to the prevention of falsified labeling.
Collapse
Affiliation(s)
- Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Urtzi Laconcha
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
- Marine Research Division, AZTI , 20110 Pasaia, Spain
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Carmen Manzano
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | | | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| |
Collapse
|
11
|
Liao Z, Wan Q, Shang X, Su J. Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella. Sci Rep 2017; 7:1184. [PMID: 28446772 PMCID: PMC5430748 DOI: 10.1038/s41598-017-01338-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/28/2017] [Indexed: 02/02/2023] Open
Abstract
Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.
Collapse
Affiliation(s)
- Zhiwei Liao
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quanyuan Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueying Shang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Su
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
12
|
Status and future perspectives of single nucleotide polymorphisms (SNPs) markers in farmed fishes: Way ahead using next generation sequencing. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
13
|
Therkildsen NO, Palumbi SR. Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Mol Ecol Resour 2016; 17:194-208. [DOI: 10.1111/1755-0998.12593] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/27/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Nina Overgaard Therkildsen
- Hopkins Marine Station; Department of Biology; Stanford University; 120 Oceanview Blvd. Pacific Grove CA 93950 USA
| | - Stephen R. Palumbi
- Hopkins Marine Station; Department of Biology; Stanford University; 120 Oceanview Blvd. Pacific Grove CA 93950 USA
| |
Collapse
|
14
|
Humble E, Thorne MAS, Forcada J, Hoffman JI. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success. BMC Res Notes 2016; 9:418. [PMID: 27562535 PMCID: PMC5000416 DOI: 10.1186/s13104-016-2209-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/06/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. RESULTS Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. CONCLUSIONS Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms.
Collapse
Affiliation(s)
- Emily Humble
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany. .,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
| | - Michael A S Thorne
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany
| |
Collapse
|
15
|
Clupeiformes’ Egg Envelope Proteins characterization: The case of Engraulis encrasicolus as a proxy for stock assessment through a novel molecular tool. Mol Phylogenet Evol 2016; 100:95-108. [DOI: 10.1016/j.ympev.2016.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 11/20/2022]
|
16
|
Niedzicka M, Fijarczyk A, Dudek K, Stuglik M, Babik W. Molecular Inversion Probes for targeted resequencing in non-model organisms. Sci Rep 2016; 6:24051. [PMID: 27046329 PMCID: PMC4820773 DOI: 10.1038/srep24051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/18/2016] [Indexed: 12/21/2022] Open
Abstract
Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples.
Collapse
Affiliation(s)
- M Niedzicka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - A Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - M Stuglik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| |
Collapse
|
17
|
Crawford DL, Oleksiak MF. Ecological population genomics in the marine environment. Brief Funct Genomics 2016; 15:342-51. [DOI: 10.1093/bfgp/elw008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
18
|
Humble E, Martinez-Barrio A, Forcada J, Trathan PN, Thorne MAS, Hoffmann M, Wolf JBW, Hoffman JI. A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them. Mol Ecol Resour 2016; 16:909-21. [DOI: 10.1111/1755-0998.12502] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 01/19/2023]
Affiliation(s)
- E. Humble
- Department of Animal Behaviour; University of Bielefeld; Postfach 100131 33501 Bielefeld Germany
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - A. Martinez-Barrio
- Science of Life Laboratories and Department of Cell and Molecular Biology; Uppsala University; Husargatan 3 75124 Uppsala Sweden
| | - J. Forcada
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - P. N. Trathan
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - M. A. S. Thorne
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - M. Hoffmann
- Max Planck Institute for Developmental Biology; Spemannstrasse 35 72076 Tübingen Germany
| | - J. B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
| | - J. I. Hoffman
- Department of Animal Behaviour; University of Bielefeld; Postfach 100131 33501 Bielefeld Germany
| |
Collapse
|
19
|
Qu H, Luo W, Lin Q. Development of SNP markers in lined seahorse (Hippocampus erectus) based on transcriptome sequencing. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0510-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Pappalardo AM, Ferrito V. A COIBar-RFLP strategy for the rapid detection of Engraulis encrasicolus in processed anchovy products. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.03.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
21
|
De Wit P, Pespeni MH, Palumbi SR. SNP genotyping and population genomics from expressed sequences - current advances and future possibilities. Mol Ecol 2015; 24:2310-23. [DOI: 10.1111/mec.13165] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/13/2015] [Accepted: 03/18/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Pierre De Wit
- Department of Biology and Environmental Sciences; University of Gothenburg; Sven Lovén Centre for Marine Science - Tjärnö; Hättebäcksvägen 7 Strömstad SE-452 96 Sweden
| | - Melissa H. Pespeni
- Department of Biology; University of Vermont; Marsh Life Science; Rm 326A 109 Carrigan Drive Burlington VT 05405 USA
| | - Stephen R. Palumbi
- Department of Biology; Stanford University; Hopkins Marine Station 120 Ocean view Blvd. Pacific Grove CA 93950 USA
| |
Collapse
|
22
|
De novo assembly and comprehensive characterization of the skeletal muscle transcriptomes of the European anchovy (Engraulis encrasicolus). Mar Genomics 2015; 20:7-9. [DOI: 10.1016/j.margen.2015.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 11/17/2022]
|
23
|
Zhao X, Yu H, Kong L, Liu S, Li Q. Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PLoS One 2014; 9:e111915. [PMID: 25369077 PMCID: PMC4219811 DOI: 10.1371/journal.pone.0111915] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/01/2014] [Indexed: 12/29/2022] Open
Abstract
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.
Collapse
Affiliation(s)
- Xuelin Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- * E-mail:
| |
Collapse
|
24
|
Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. THE BIOLOGICAL BULLETIN 2014; 227:117-132. [PMID: 25411371 DOI: 10.1086/bblv227n2p117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past few years, technological advances have facilitated giant leaps forward in our ability to generate genome-wide molecular data, offering exciting opportunities for gaining new insights into the ecology and evolution of species where genomic information is still limited. Marine fishes are valuable organisms for advancing our understanding of evolution on historical and contemporary time scales, and here we highlight areas in which research on these species is likely to be particularly important in the near future. These include possibilities for gaining insights into processes on ecological time scales, identifying genomic signatures associated with population divergence under gene flow, and determining the genetic basis of phenotypic traits. We also consider future challenges pertaining to the implementation of genome-wide coverage through next-generation sequencing and genotyping methods in marine fishes. Complications associated with fast decay of linkage disequilibrium, as expected for species with large effective population sizes, and the possibility that adaptation is associated with both soft selective sweeps and polygenic selection, leaving complex genomic signatures in natural populations, are likely to challenge future studies. However, the combination of high genome coverage and new statistical developments offers promising solutions. Thus, the next generation of studies is likely to truly facilitate the transition from population genetics to population genomics in marine fishes. This transition will advance our understanding of basic evolutionary processes and will offer new possibilities for conservation and management of valuable marine resources.
Collapse
Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark;
| | | | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| |
Collapse
|
25
|
El Mujtar VA, Gallo LA, Lang T, Garnier-Géré P. Development of genomic resources forNothofagusspecies using next-generation sequencing data. Mol Ecol Resour 2014; 14:1281-95. [DOI: 10.1111/1755-0998.12276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/23/2014] [Accepted: 04/28/2014] [Indexed: 11/30/2022]
Affiliation(s)
- V. A. El Mujtar
- Unidad de Genética Ecológica y Mejoramiento Forestal; Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Bariloche; Modesta Victoria 4450 (8400) Bariloche Río Negro Argentina
- INRA; UMR 1202 Biodiversity Genes & Communities; F- 33610 Cestas France
- UMR1202 Biodiversity Genes & Communities; University of Bordeaux; Bordeaux F-33400 Talence France
| | - L. A. Gallo
- Unidad de Genética Ecológica y Mejoramiento Forestal; Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Bariloche; Modesta Victoria 4450 (8400) Bariloche Río Negro Argentina
| | - T. Lang
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla Yunnan 666303 China
| | - P. Garnier-Géré
- INRA; UMR 1202 Biodiversity Genes & Communities; F- 33610 Cestas France
- UMR1202 Biodiversity Genes & Communities; University of Bordeaux; Bordeaux F-33400 Talence France
| |
Collapse
|