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Fontaine R, Rahmad Royan M, Henkel C, Hodne K, Ager-Wick E, Weltzien FA. Pituitary multi-hormone cells in mammals and fish: history, origin, and roles. Front Neuroendocrinol 2022; 67:101018. [PMID: 35870647 DOI: 10.1016/j.yfrne.2022.101018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/10/2022] [Accepted: 07/18/2022] [Indexed: 11/04/2022]
Abstract
The vertebrate pituitary is a dynamic organ, capable of adapting its hormone secretion to different physiological demands. In this context, endocrinologists have debated for the past 40 years if endocrine cells are mono- or multi-hormonal. Since its establishment, the dominant "one cell, one hormone" model has been continuously challenged. In mammals, the use of advanced multi-staining approaches, sensitive gene expression techniques, and the analysis of tumor tissues have helped to quickly demonstrate the existence of pituitary multi-hormone cells. In fishes however, only recent advances in imaging and transcriptomics have enabled the identification of such cells. In this review, we first describe the history of the discovery of cells producing multiple hormones in mammals and fishes. We discuss the technical limitations that have led to uncertainties and debates. Then, we present the current knowledge and hypotheses regarding their origin and biological role, which provides a comprehensive review of pituitary plasticity.
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Affiliation(s)
- Romain Fontaine
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway.
| | - Muhammad Rahmad Royan
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Christiaan Henkel
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Kjetil Hodne
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Eirill Ager-Wick
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Finn-Arne Weltzien
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway.
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He P, Zhu P, Wei P, Zhuo X, Ma Y, Chen X, Lin Y, Xu Y, Luo H, Peng J. Gonadal transcriptomic analysis and differentially expressed genes between the testes and ovaries in Trachinotus ovatus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Watanabe K, Konno N, Nakamachi T, Matsuda K. Intracerebroventricular administration of α-melanocyte-stimulating hormone (α-MSH) enhances thigmotaxis and induces anxiety-like behavior in the goldfish Carassius auratus. Peptides 2021; 145:170623. [PMID: 34375685 DOI: 10.1016/j.peptides.2021.170623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022]
Abstract
α-Melanocyte-stimulating hormone (α-MSH) is a body pigmentation-regulating hormone secreted from the intermediate lobe of the pituitary in vertebrates. It is also produced in the brain, and acts as an anorexigenic neuropeptide involved in feeding regulation. In rodents, intracerebroventricular (ICV) administration of α-MSH has been shown to affect not only feeding behavior, but also psychomotor activity. However, there is still no information regarding the psychophysiological effects of α-MSH on behavior in fish. Therefore, we examined the effect of synthetic α-MSH on psychomotor activity in goldfish. Since this species prefers the edge to the central area of a tank, we used this as a preference test for assessing psychomotor activity. When α-MSH was administered ICV at 1 and 10 pmol g-1 body weight (BW), the time spent in the edge area of a tank was prolonged at 10 pmol g-1 BW. However, α-MSH at these doses did not affect locomotor activity. The action of α-MSH mimicked those of FG-7142 (a central-type benzodiazepine receptor (CBR) inverse agonist with an anxiogenic effect) at 10 pmol g-1 BW and melanotan II (a melanocortin 4 receptor (MC4R) agonist) at 50 pmol g-1 BW, whereas ICV administration of tofisopam (a CBR agonist with an anxiolytic effect) at 10 pmol g-1 BW prolonged the time spent in the central area. The anxiogenic-like effect of α-MSH was abolished by treatment with the MC4R antagonist HS024 at 50 pmol g-1 BW. These data indicate that α-MSH affects psychomotor activity in goldfish, and exerts an anxiogenic-like effect via the MC4R-signaling pathway.
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Affiliation(s)
- Keisuke Watanabe
- Laboratory of Regulatory Biology, Graduate School of Innovative Life Sciences, University of Toyama, Toyama, 930-8555, Japan
| | - Norifumi Konno
- Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan; Laboratory of Regulatory Biology, Faculty of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Tomoya Nakamachi
- Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan; Laboratory of Regulatory Biology, Faculty of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan
| | - Kouhei Matsuda
- Laboratory of Regulatory Biology, Graduate School of Innovative Life Sciences, University of Toyama, Toyama, 930-8555, Japan; Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan; Laboratory of Regulatory Biology, Faculty of Science, Academic Assembly, University of Toyama, Toyama, 930-8555, Japan.
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Characterization of hormone-producing cell types in the teleost pituitary gland using single-cell RNA-seq. Sci Data 2021; 8:279. [PMID: 34711832 PMCID: PMC8553774 DOI: 10.1038/s41597-021-01058-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 09/09/2021] [Indexed: 11/08/2022] Open
Abstract
The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism, and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types remain to be resolved. We have therefore used single-cell sequencing to generate gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, we define 15 and 16 distinct cell types in the female and male pituitary, respectively, of which ten are involved in the production of a single peptide hormone. Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general. Measurement(s) | RNA-seq gene expression profiling assay | Technology Type(s) | tag based single cell RNA sequencing | Factor Type(s) | sex | Sample Characteristic - Organism | Oryzias latipes | Sample Characteristic - Environment | fresh water aquarium |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.16592621
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Bertolini F, Jørgensen MGP, Henkel C, Dufour S, Tomkiewicz J. Unravelling the changes during induced vitellogenesis in female European eel through RNA-Seq: What happens to the liver? PLoS One 2020; 15:e0236438. [PMID: 32790680 PMCID: PMC7425897 DOI: 10.1371/journal.pone.0236438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/06/2020] [Indexed: 11/24/2022] Open
Abstract
The life cycle of European eel (Anguilla anguilla), a catadromous species, is complex and enigmatic. In nature, during the silvering process prior to their long spawning migration, reproductive development is arrested, and they cease feeding. In studies of reproduction using hormonal induction, eels are equivalently not feed. Therefore, in female eels that undergo vitellogenesis, the liver plays different, essential roles being involved both in vitellogenins synthesis and in reallocating resources for the maintenance of vital functions, performing the transoceanic reproductive migration and completing reproductive development. The present work aimed at unravelling the major transcriptomic changes that occur in the liver during induced vitellogenesis in female eels. mRNA-Seq data from 16 animals (eight before induced vitellogenesis and eight after nine weeks of hormonal treatment) were generated and differential expression analysis was performed comparing the two groups. This analysis detected 1,328 upregulated and 1,490 downregulated transcripts. Overrepresentation analysis of the upregulated genes included biological processes related to biosynthesis, response to estrogens, mitochondrial activity and localization, while downregulated genes were enriched in processes related to morphogenesis and development of several organs and tissues, including liver and immune system. Among key genes, the upregulated ones included vitellogenin genes (VTG1 and VTG2) that are central in vitellogenesis, together with ESR1 and two novel genes not previously investigated in European eel (LMAN1 and NUPR1), which have been linked with reproduction in other species. Moreover, several upregulated genes, such as CYC1, ELOVL5, KARS and ACSS1, are involved in the management of the effect of fasting and NOTCH, VEGFA and NCOR are linked with development, autophagy and liver maintenance in other species. These results increase the understanding of the molecular changes that occur in the liver during vitellogenesis in this complex and distinctive fish species, bringing new insights on European eel reproduction and broodstock management.
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Affiliation(s)
- Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
| | | | - Christiaan Henkel
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Sylvie Dufour
- Laboratory BOREA, Museum National d’Histoire Naturelle, CNRS, Sorbonne University, Paris, France
| | - Jonna Tomkiewicz
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
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De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. PLoS One 2019; 14:e0218085. [PMID: 31188893 PMCID: PMC6561569 DOI: 10.1371/journal.pone.0218085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/25/2019] [Indexed: 12/18/2022] Open
Abstract
Paralogues pairs are more frequently observed in eels (Anguilla sp.) than in other teleosts. The paralogues often show low phylogenetic distances; however, they have been assigned to the third round of whole genome duplication (WGD), shared by all teleosts (3R), due to their conserved synteny. The apparent contradiction of low phylogenetic difference and 3R conserved synteny led us to study the duplicated gene complement of the freshwater eels. With this aim, we assembled de novo transcriptomes of two highly relevant freshwater eel species: The European (Anguilla anguilla) and the Japanese eel (Anguilla japonica). The duplicated gene complement was analysed in these transcriptomes, and in the genomes and transcriptomes of other Actinopterygii species. The study included an assessment of neutral genetic divergence (4dTv), synteny, and the phylogenetic origins and relationships of the duplicated gene complements. The analyses indicated a high accumulation of duplications (1217 paralogue pairs) among freshwater eel genes, which may have originated in a WGD event after the Elopomorpha lineage diverged from the remaining teleosts, and thus not at the 3R. However, very similar results were observed in the basal Osteoglossomorpha and Clupeocephala branches, indicating that the specific genomic regions of these paralogues may still have been under tetrasomic inheritance at the split of the teleost lineages. Therefore, two potential hypotheses may explain the results: i) The freshwater eel lineage experienced an additional WGD to 3R, and ii) Some duplicated genomic regions experienced lineage specific rediploidization after 3R in the ancestor to freshwater eels. The supporting/opposing evidence for both hypotheses is discussed.
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Mohamed AR, Verbyla KL, Al-Mamun HA, McWilliam S, Evans B, King H, Kube P, Kijas JW. Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon. BMC Genomics 2019; 20:139. [PMID: 30770720 PMCID: PMC6377724 DOI: 10.1186/s12864-019-5525-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 02/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts. RESULTS We report genome wide association studies (GWAS) using fish measured for sexual maturation in freshwater or the marine environment. Genotypic data from a custom 50 K single nucleotide polymorphism (SNP) array was used to identify 13 significantly associated SNP for freshwater maturation with the most strongly associated on chromosomes 10 and 11. A higher number of associations (48) were detected for marine maturation, and the two peak loci were found to be the same for both traits. The number and broad distribution of GWAS hits confirmed a highly polygenetic nature, and GWAS performed separately within males and females revealed sex specific genetic behaviour for loci co-located with positional candidate genes phosphatidylinositol-binding clathrin assembly protein-like (picalm) and membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (magi2). CONCLUSIONS The results extend earlier work and have implications for future applied breeding strategies to delay maturation in this important aquaculture species.
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Affiliation(s)
- Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia Brisbane, 4067, Australia.,Zoology Department, Faculty of Science, Benha University, Benha, 13518, Egypt
| | - Klara L Verbyla
- Commonwealth Scientific and Industrial Research Organisation Data 61, Canberra, Australian Capital Territory, 2601, Australia
| | - Hawlader A Al-Mamun
- Commonwealth Scientific and Industrial Research Organisation Data 61, Canberra, Australian Capital Territory, 2601, Australia
| | - Sean McWilliam
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia Brisbane, 4067, Australia
| | - Bradley Evans
- Tassal Operations Pty Ltd, Hobart, Tasmania, 7001, Australia
| | - Harry King
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Hobart, Tasmania, 7004, Australia
| | - Peter Kube
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Hobart, Tasmania, 7004, Australia
| | - James W Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia Brisbane, 4067, Australia.
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Yada T, Mekuchi M, Ojima N. Molecular biology and functional genomics of immune-endocrine interactions in the Japanese eel, Anguilla japonica. Gen Comp Endocrinol 2018; 257:272-279. [PMID: 29108728 DOI: 10.1016/j.ygcen.2017.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 10/03/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
Abstract
Immune-endocrine interactions are an important pathogen resistance mechanism in fish. We review the immune-endocrine interactions in the Japanese eel, Anguilla japonica, with special reference to high throughput gene sequencing. These data may be relevant to the significant decrease in the eel harvest in recent years and will aid in the selection of appropriate disease-resistant strains for aquaculture. More than 1000 sequences that whose expression in elvers responded to air exposure were identified through comprehensive gene expression analysis using next-generation sequencing. These included transcription factors within the MAPK pathway. Significant changes in expression after air exposure were detected by quantitative polymerase chain reaction analysis in many genes related to disease resistance. These factors include innate immune system factors and cytokines that interact with the endocrine system during the stress response. Other applications of immune-endocrine interactions in eel culture are discussed.
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Affiliation(s)
- Takashi Yada
- Freshwater Fisheries Research Center, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Nikko, Japan.
| | - Miyuki Mekuchi
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Nobuhiko Ojima
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
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Jansen HJ, Liem M, Jong-Raadsen SA, Dufour S, Weltzien FA, Swinkels W, Koelewijn A, Palstra AP, Pelster B, Spaink HP, Thillart GEVD, Dirks RP, Henkel CV. Rapid de novo assembly of the European eel genome from nanopore sequencing reads. Sci Rep 2017; 7:7213. [PMID: 28775309 PMCID: PMC5543108 DOI: 10.1038/s41598-017-07650-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/28/2017] [Indexed: 02/07/2023] Open
Abstract
We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2 Mbp) and structural quality. This combination of affordable nanopore sequencing and light weight assembly promises to make high-quality genomic resources accessible for many non-model plants and animals.
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Affiliation(s)
| | - Michael Liem
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Sylvie Dufour
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, UCN, UA, Paris, France
| | - Finn-Arne Weltzien
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Basic Science and Aquatic Medicine, Oslo, Norway
| | | | | | - Arjan P Palstra
- Animal Breeding and Genomics Centre, Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Bernd Pelster
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | | | - Christiaan V Henkel
- Institute of Biology, Leiden University, Leiden, The Netherlands.
- University of Applied Sciences Leiden, Leiden, The Netherlands.
- Generade Centre of Expertise in Genomics, Leiden, The Netherlands.
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10
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Kolder ICRM, van der Plas-Duivesteijn SJ, Tan G, Wiegertjes GF, Forlenza M, Guler AT, Travin DY, Nakao M, Moritomo T, Irnazarow I, den Dunnen JT, Anvar SY, Jansen HJ, Dirks RP, Palmblad M, Lenhard B, Henkel CV, Spaink HP. A full-body transcriptome and proteome resource for the European common carp. BMC Genomics 2016; 17:701. [PMID: 27590662 PMCID: PMC5009708 DOI: 10.1186/s12864-016-3038-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/24/2016] [Indexed: 12/01/2022] Open
Abstract
Background The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies. Results Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data. Conclusions The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I C R M Kolder
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.,Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333, CA, Leiden, The Netherlands
| | | | - G Tan
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - G F Wiegertjes
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - M Forlenza
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - A T Guler
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands
| | - D Y Travin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, GSP-1, Moscow, Russia
| | - M Nakao
- Laboratory of Marine Biochemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan
| | - T Moritomo
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan
| | - I Irnazarow
- Polish Academy of Sciences, Ichthyobiology and Aquaculture Unit, Gołysz Zaborze, Kalinowa 2, 43-520, Chybie, Poland
| | - J T den Dunnen
- Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - S Y Anvar
- Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - H J Jansen
- ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands
| | - R P Dirks
- ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands
| | - M Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands
| | - B Lenhard
- Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - C V Henkel
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands
| | - H P Spaink
- Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.
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Ager-Wick E, Henkel CV, Haug TM, Weltzien FA. Using normalization to resolve RNA-Seq biases caused by amplification from minimal input. Physiol Genomics 2014; 46:808-20. [PMID: 25228281 DOI: 10.1152/physiolgenomics.00196.2013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RNA-Seq has become a widely used method to study transcriptomes, and it is now possible to perform RNA-Seq on almost any sample. Nevertheless, samples obtained from small cell populations are particularly challenging, as biases associated with low amounts of input RNA can have strong and detrimental effects on downstream analyses. Here we compare different methods to normalize RNA-Seq data obtained from minimal input material. Using RNA from isolated medaka pituitary cells, we have amplified material from six samples before sequencing. Both synthetic and real data are used to evaluate different normalization methods to obtain a robust and reliable pipeline for analysis of RNA-Seq data from samples with very limited input material. The analysis outlined here shows that quantile normalization outperforms other more commonly used normalization procedures when using amplified RNA as input and will benefit researchers employing low amounts of RNA in similar experiments.
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Affiliation(s)
- Eirill Ager-Wick
- Weltzien Laboratory, Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Christiaan V Henkel
- Weltzien Laboratory, Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway; Institute of Biology, Leiden University, Leiden, The Netherlands; and
| | - Trude M Haug
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Finn-Arne Weltzien
- Weltzien Laboratory, Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, Oslo, Norway; Department of Biosciences, University of Oslo, Oslo, Norway
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12
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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