1
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Zhang L, Zhou J. Zebrafish: A smart tool for heart disease research. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37824489 DOI: 10.1111/jfb.15585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
The increasing prevalence of heart disease poses a significant threat to human survival and safety. However, the current treatments available for heart disease are quite limited. Therefore, it is of great importance to utilize suitable animal models that can accurately simulate the physiological characteristics of heart disease. This would help improve our understanding of this disease and aid in the development of new treatment methods and drugs. Zebrafish hearts not only exhibit similarities to mammalian hearts, but they also share ~70% of homologous genes with humans. Utilizing zebrafish as an alternative to costly and time-consuming mammalian models offers numerous advantages. Zebrafish models can be easily established and maintained, and compound screening and genetic methods allow for the creation of various economical and easily controlled zebrafish and zebrafish embryonic heart disease models in a short period of time. Consequently, zebrafish have become a powerful tool for exploring the pathological mechanisms of heart disease and identifying new effective genes. In this review, we summarize recent studies on different zebrafish models of heart disease. We also describe the techniques and protocols used to develop zebrafish models of myocardial infarction, heart failure, and congenital heart disease, including surgical procedures, forward and reverse genetics, as well as drug and combination screening. This review aims to promote the utilization of zebrafish models in investigating diverse pathological mechanisms of heart disease, enhancing our knowledge and comprehension of heart disease, and offering novel insights and objectives for exploring the prevention and treatment of heart disease.
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Affiliation(s)
- Lantian Zhang
- Education Branch, Chongqing Publishing Group, Chongqing, China
| | - Jinrun Zhou
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
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2
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Chothani S, Ho L, Schafer S, Rackham O. Discovering microproteins: making the most of ribosome profiling data. RNA Biol 2023; 20:943-954. [PMID: 38013207 PMCID: PMC10730196 DOI: 10.1080/15476286.2023.2279845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA sequencing and encoded translated regions inferred using sequence-based detection of start and stop combinations longer than 100 amino-acids to prevent false positives. This has led to small ORFs (smORFs) and their encoded proteins left un-annotated. Ribo-seq allows deciphering translated regions from untranslated irrespective of the length. In this review, we describe the power of Ribo-seq data in detection of smORFs while discussing the major challenge posed by data-quality, -depth and -sparseness in identifying the start and end of smORF translation. In particular, we outline smORF cataloguing efforts in humans and the large differences that have arisen due to variation in data, methods and assumptions. Although current versions of smORF reference sets can already be used as a powerful tool for hypothesis generation, we recommend that future editions should consider these data limitations and adopt unified processing for the community to establish a canonical catalogue of translated smORFs.
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
- The Alan Turing Institute, The British Library, London, UK
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3
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Di Biagio C, Dellacqua Z, Martini A, Huysseune A, Scardi M, Witten PE, Boglione C. A Baseline for Skeletal Investigations in Medaka ( Oryzias latipes): The Effects of Rearing Density on the Postcranial Phenotype. Front Endocrinol (Lausanne) 2022; 13:893699. [PMID: 35846331 PMCID: PMC9281570 DOI: 10.3389/fendo.2022.893699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Oryzias latipes is increasingly used as a model in biomedical skeletal research. The standard approach is to generate genetic variants with particular skeletal phenotypes which resemble skeletal diseases in humans. The proper diagnosis of skeletal variation is key for this type of research. However, even laboratory rearing conditions can alter skeletal phenotypes. The subject of this study is the link between skeletal phenotypes and rearing conditions. Thus, wildtype medaka were reared from hatching to an early juvenile stage at low (LD: 5 individuals/L), medium (MD: 15 individuals/L), and high (HD: 45 individuals/L) densities. The objectives of the study are: (I) provide a comprehensive overview of the postcranial skeletal elements in medaka; (II) evaluate the effects of rearing density on specific meristic counts and on the variability in type and incidence of skeletal anomalies; (III) define the best laboratory settings to obtain a skeletal reference for a sound evaluation of future experimental conditions; (IV) contribute to elucidating the structural and cellular changes related to the onset of skeletal anomalies. The results from this study reveal that rearing densities greater than 5 medaka/L reduce the animals' growth. This reduction is related to decreased mineralization of dermal (fin rays) and perichondral (fin supporting elements) bone. Furthermore, high density increases anomalies affecting the caudal fin endoskeleton and dermal rays, and the preural vertebral centra. A series of static observations on Alizarin red S whole mount-stained preural fusions provide insights into the etiology of centra fusion. The fusion of preural centra involves the ectopic formation of bony bridges over the intact intervertebral ligament. An apparent consequence is the degradation of the intervertebral ligaments and the remodeling and reshaping of the fused vertebral centra into a biconoid-shaped centrum. From this study it can be concluded that it is paramount to take into account the rearing conditions, natural variability, skeletal phenotypic plasticity, and the genetic background along with species-specific peculiarities when screening for skeletal phenotypes of mutant or wildtype medaka.
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Affiliation(s)
- Claudia Di Biagio
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
- Laboratory of Evolutionary Developmental Biology, Gent University, Department of Biology, Gent, Belgium
| | - Zachary Dellacqua
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
- Aquaculture Research Group (GIA), Universidad de Las Palmas de Gran Canaria, Institute of Sustainable Aquaculture and Marine Ecosystems (ECOAQUA), Las Palmas, Spain
| | - Arianna Martini
- Laboratory of Experimental Ecology and Aquaculture, University of Rome ‘Tor Vergata’, Department of Biology, Rome, Italy
| | - Ann Huysseune
- Laboratory of Evolutionary Developmental Biology, Gent University, Department of Biology, Gent, Belgium
| | - Michele Scardi
- Laboratory of Experimental Ecology and Aquaculture, University of Rome ‘Tor Vergata’, Department of Biology, Rome, Italy
| | - Paul Eckhard Witten
- Laboratory of Evolutionary Developmental Biology, Gent University, Department of Biology, Gent, Belgium
| | - Clara Boglione
- Laboratory of Experimental Ecology and Aquaculture, University of Rome ‘Tor Vergata’, Department of Biology, Rome, Italy
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4
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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.
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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.
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5
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Rao WQ, Kalogeropoulos K, Allentoft ME, Gopalakrishnan S, Zhao WN, Workman CT, Knudsen C, Jiménez-Mena B, Seneci L, Mousavi-Derazmahalleh M, Jenkins TP, Rivera-de-Torre E, Liu SQ, Laustsen AH. The rise of genomics in snake venom research: recent advances and future perspectives. Gigascience 2022; 11:6562531. [PMID: 35365832 PMCID: PMC8975721 DOI: 10.1093/gigascience/giac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 12/12/2022] Open
Abstract
Snake venoms represent a danger to human health, but also a gold mine of bioactive proteins that can be harnessed for drug discovery purposes. The evolution of snakes and their venom has been studied for decades, particularly via traditional morphological and basic genetic methods alongside venom proteomics. However, while the field of genomics has matured rapidly over the past 2 decades, owing to the development of next-generation sequencing technologies, snake genomics remains in its infancy. Here, we provide an overview of the state of the art in snake genomics and discuss its potential implications for studying venom evolution and toxinology. On the basis of current knowledge, gene duplication and positive selection are key mechanisms in the neofunctionalization of snake venom proteins. This makes snake venoms important evolutionary drivers that explain the remarkable venom diversification and adaptive variation observed in these reptiles. Gene duplication and neofunctionalization have also generated a large number of repeat sequences in snake genomes that pose a significant challenge to DNA sequencing, resulting in the need for substantial computational resources and longer sequencing read length for high-quality genome assembly. Fortunately, owing to constantly improving sequencing technologies and computational tools, we are now able to explore the molecular mechanisms of snake venom evolution in unprecedented detail. Such novel insights have the potential to affect the design and development of antivenoms and possibly other drugs, as well as provide new fundamental knowledge on snake biology and evolution.
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Affiliation(s)
- Wei-Qiao Rao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark.,Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Konstantinos Kalogeropoulos
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia.,Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350, Copenhagen, Denmark
| | - Wei-Ning Zhao
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Cecilie Knudsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Belén Jiménez-Mena
- DTU Aqua, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Lorenzo Seneci
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, 6102, Bentley Perth, Australia
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Si-Qi Liu
- Department of Mass Spectrometry, Beijing Genomics Institute-Research, 518083, Shenzhen, China
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
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6
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Sehgal P, Mathew S, Sivadas A, Ray A, Tanwar J, Vishwakarma S, Ranjan G, Shamsudheen KV, Bhoyar RC, Pateria A, Leonard E, Lalwani M, Vats A, Pappuru RR, Tyagi M, Jakati S, Sengupta S, B K B, Chakrabarti S, Kaur I, Motiani RK, Scaria V, Sivasubbu S. LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy. EMBO J 2021; 40:e107134. [PMID: 34180064 PMCID: PMC8327952 DOI: 10.15252/embj.2020107134] [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: 11/06/2020] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 12/29/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) are emerging as key regulators of endothelial cell function. Here, we investigated the role of a novel vascular endothelial‐associated lncRNA (VEAL2) in regulating endothelial permeability. Precise editing of veal2 loci in zebrafish (veal2gib005Δ8/+) induced cranial hemorrhage. In vitro and in vivo studies revealed that veal2 competes with diacylglycerol for interaction with protein kinase C beta‐b (Prkcbb) and regulates its kinase activity. Using PRKCB2 as bait, we identified functional ortholog of veal2 in humans from HUVECs and named it as VEAL2. Overexpression and knockdown of VEAL2 affected tubulogenesis and permeability in HUVECs. VEAL2 was differentially expressed in choroid tissue in eye and blood from patients with diabetic retinopathy, a disease where PRKCB2 is known to be hyperactivated. Further, VEAL2 could rescue the effects of PRKCB2‐mediated turnover of endothelial junctional proteins thus reducing hyperpermeability in hyperglycemic HUVEC model of diabetic retinopathy. Based on evidence from zebrafish and hyperglycemic HUVEC models and diabetic retinopathy patients, we report a hitherto unknown VEAL2 lncRNA‐mediated regulation of PRKCB2, for modulating junctional dynamics and maintenance of endothelial permeability.
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Affiliation(s)
- Paras Sehgal
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ambily Sivadas
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Arjun Ray
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Jyoti Tanwar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India.,Laboratory of Calciomics and Systemic Pathophysiology, Regional Center for Biotechnology, Faridabad, India
| | - Sushma Vishwakarma
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Gyan Ranjan
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhishek Pateria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Elvin Leonard
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mukesh Lalwani
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajeev R Pappuru
- Kannuri Santhamma Centre for Retina and Vitreous, L V Prasad Eye Institute, Hyderabad, India
| | - Mudit Tyagi
- Kannuri Santhamma Centre for Retina and Vitreous, L V Prasad Eye Institute, Hyderabad, India
| | - Saumya Jakati
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | - Inderjeet Kaur
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Center for Biotechnology, Faridabad, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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7
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King AC, Gut M, Zenker AK. Shedding new light on early sex determination in zebrafish. Arch Toxicol 2020; 94:4143-4158. [PMID: 32975586 PMCID: PMC7655572 DOI: 10.1007/s00204-020-02915-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/17/2020] [Indexed: 01/10/2023]
Abstract
In contrast to established zebrafish gene annotations, the question of sex determination has still not been conclusively clarified for developing zebrafish, Danio rerio, larvae, 28 dpf or earlier. Recent studies indicate polygenic sex determination (PSD), with the genes being distributed throughout the genome. Early genetic markers of sex in zebrafish help unravel co-founding sex-related differences to apply to human health and environmental toxicity studies. A qPCR-based method was developed for six genes: cytochrome P450, family 17, subfamily A, polypeptide 1 (cyp17a1); cytochrome P450, family 19, subfamily A, polypeptide 1a (cyp19a1a); cytochrome P450, family 19, subfamily A, polypeptides 1b (cyp19a1b); vitellogenin 1 (vtg1); nuclear receptor subfamily 0, group B, member 1 (nr0b1), sry (sex-determining region Y)-box 9b (sox9b) and actin, beta 1 (actb1), the reference gene. Sry-box 9a (Sox9a), insulin-like growth factor 3 (igf3) and double sex and mab-3 related transcription factor 1 (dmrt1), which are also known to be associated with sex determination, were used in gene expression tests. Additionally, Next-Generation-Sequencing (NGS) sequenced the genome of two adult female and male and two juveniles. PCR analysis of adult zebrafish revealed sex-specific expression of cyp17a1, cyp19a1a, vtg1, igf3 and dmrt1, the first four strongly expressed in female zebrafish and the last one highly expressed in male conspecifics. From NGS, nine female and four male-fated genes were selected as novel for assessing zebrafish sex, 28 dpf. Differences in transcriptomes allowed allocation of sex-specific genes also expressed in juvenile zebrafish.
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Affiliation(s)
- Alex C King
- FHNW, University of Applied Sciences and Arts North-Western Switzerland, School of Life Sciences, Institute for Ecopreneurship, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Michelle Gut
- FHNW, University of Applied Sciences and Arts North-Western Switzerland, School of Life Sciences, Institute for Ecopreneurship, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Armin K Zenker
- FHNW, University of Applied Sciences and Arts North-Western Switzerland, School of Life Sciences, Institute for Ecopreneurship, Hofackerstrasse 30, 4132, Muttenz, Switzerland.
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8
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Liu X, Zeng S, Liu S, Wang G, Lai H, Zhao X, Bi S, Guo D, Chen X, Yi H, Su Y, Zhang Y, Li G. Identifying the Related Genes of Muscle Growth and Exploring the Functions by Compensatory Growth in Mandarin Fish ( Siniperca chuatsi). Front Physiol 2020; 11:553563. [PMID: 33117188 PMCID: PMC7552573 DOI: 10.3389/fphys.2020.553563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/31/2020] [Indexed: 01/16/2023] Open
Abstract
How organisms display many different biochemical, physiological processes through genes expression and regulatory mechanisms affecting muscle growth is a central issue in growth and development. In Siniperca chuatsi, the growth-related genes and underlying relevant mechanisms are poorly understood, especially for difference of body sizes and compensatory growth performance. Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. Results showed that 8,942 different expression genes (DEGs) were identified after calculating the RPKM. The DEGs involved in GH-IGF pathways, protein synthesis, ribosome synthesis and energy metabolisms, which were expressed significantly higher in small individuals (S) than large fish (L). In repletion feeding and compensatory growth experiments, eight more significant DEGs were used for further research (GHR2, IGFR1, 4ebp, Mhc, Mlc, Myf6, MyoD, troponin). When food was plentiful, eight genes participated in and promoted growth and muscle synthesis, respectively. Starvation can be shown to inhibit the expression of Mhc, Mlc and troponin, and high expression of GHR2, IGFR1, and 4ebp inhibited growth. Fasting promoted the metabolic actions of GHR2, IGFR1, and 4ebp rather than the growth-promoting actions. MyoD can sense and regulate the hunger, which also worked with Mhc and Mlc to accelerate the compensatory growth of S. chuatsi. This study is helpful to understand the regulation mechanisms of muscle growth-related genes. The elected genes will contribute to the selective breeding in future as candidate genes.
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Affiliation(s)
- Xuange Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shuang Zeng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shuang Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Gongpei Wang
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Han Lai
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiaopin Zhao
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Sheng Bi
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Dingli Guo
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiaoli Chen
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Huadong Yi
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yuqin Su
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yong Zhang
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Guifeng Li
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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9
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Hau HTA, Ogundele O, Hibbert AH, Monfries CAL, Exelby K, Wood NJ, Nevarez-Mejia J, Carbajal MA, Fleck RA, Dermit M, Mardakheh FK, Williams-Ward VC, Pipalia TG, Conte MR, Hughes SM. Maternal Larp6 controls oocyte development, chorion formation and elevation. Development 2020; 147:dev187385. [PMID: 32054660 PMCID: PMC7055395 DOI: 10.1242/dev.187385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/23/2020] [Indexed: 12/19/2022]
Abstract
La-related protein 6 (Larp6) is a conserved RNA-binding protein found across eukaryotes that has been suggested to regulate collagen biogenesis, muscle development, ciliogenesis, and various aspects of cell proliferation and migration. Zebrafish have two Larp6 family genes: larp6a and larp6b Viable and fertile single and double homozygous larp6a and larp6b zygotic mutants revealed no defects in muscle structure, and were indistinguishable from heterozygous or wild-type siblings. However, larp6a mutant females produced eggs with chorions that failed to elevate fully and were fragile. Eggs from larp6b single mutant females showed minor chorion defects, but chorions from eggs laid by larp6a;larp6b double mutant females were more defective than those from larp6a single mutants. Electron microscopy revealed defective chorionogenesis during oocyte development. Despite this, maternal zygotic single and double mutants were viable and fertile. Mass spectrometry analysis provided a description of chorion protein composition and revealed significant reductions in a subset of zona pellucida and lectin-type proteins between wild-type and mutant chorions that paralleled the severity of the phenotype. We conclude that Larp6 proteins are required for normal oocyte development, chorion formation and egg activation.
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Affiliation(s)
- Hoi Ting A Hau
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Oluwaseun Ogundele
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Andrew H Hibbert
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Clinton A L Monfries
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Katherine Exelby
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Natalie J Wood
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Jessica Nevarez-Mejia
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | | | - Roland A Fleck
- Centre for Ultrastructural Imaging, King's College London, London SE1 1UL, UK
| | - Maria Dermit
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Faraz K Mardakheh
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK
| | - Victoria C Williams-Ward
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Tapan G Pipalia
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Simon M Hughes
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
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10
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Bai C, Tang M. Toxicological study of metal and metal oxide nanoparticles in zebrafish. J Appl Toxicol 2019; 40:37-63. [DOI: 10.1002/jat.3910] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Changcun Bai
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education; School of Public HealthSoutheast University Nanjing People's Republic of China
| | - Meng Tang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education; School of Public HealthSoutheast University Nanjing People's Republic of China
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11
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Giffen KP, Liu H, Kramer KL, He DZ. Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. Front Neurosci 2019; 13:1117. [PMID: 31680844 PMCID: PMC6813431 DOI: 10.3389/fnins.2019.01117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Non-mammalian vertebrates, including zebrafish, retain the ability to regenerate hair cells (HCs) due to unknown molecular mechanisms that regulate proliferation and conversion of non-sensory supporting cells (nsSCs) to HCs. This regenerative capacity is not conserved in mammals. Identification of uniquely expressed orthologous genes in zebrafish nsSCs may reveal gene candidates involved in the proliferation and transdifferentiation of zebrafish nsSCs to HCs in the inner ear. A list of orthologous protein-coding genes was generated based on an Ensembl Biomart comparison of the zebrafish and mouse genomes. Our previously published RNA-seq-based transcriptome datasets of isolated inner ear zebrafish nsSCs and HCs, and mouse non-sensory supporting pillar and Deiters’ cells, and HCs, were merged to analyze gene expression patterns between the two species. Out of 17,498 total orthologs, 11,752 were expressed in zebrafish nsSCs and over 10,000 orthologs were expressed in mouse pillar and Deiters’ cells. Differentially expressed genes common among the zebrafish nsSCs and mouse pillar and Deiters’ cells, compared to species-specific HCs, included 306 downregulated and 314 upregulated genes; however, over 1,500 genes were uniquely upregulated in zebrafish nsSCs. Functional analysis of genes uniquely expressed in nsSCs identified several transcription factors associated with cell fate determination, cell differentiation and nervous system development, indicating inherent molecular properties of nsSCs that promote self-renewal and transdifferentiation into new HCs. Our study provides a means of characterizing these orthologous genes, involved in proliferation and transdifferentiation of nsSCs to HCs in zebrafish, which may lead to identification of potential targets for HC regeneration in mammals.
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Affiliation(s)
- Kimberlee P Giffen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - Kenneth L Kramer
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
| | - David Z He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States
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12
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Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Common and distinct transcriptional signatures of mammalian embryonic lethality. Nat Commun 2019; 10:2792. [PMID: 31243271 PMCID: PMC6594971 DOI: 10.1038/s41467-019-10642-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.
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Affiliation(s)
- John E Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Richard J White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicole Staudt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ian Packham
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cecilia Mazzeo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Green
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emma Siragher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Irene Papatheodoru
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Stefan H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Wolfgang J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Antonella Galli
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Myriam Hemberger
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Derek L Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Camena Bioscience, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Elizabeth Robertson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - James C Smith
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Timothy Mohun
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
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13
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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14
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Xiong J, Lv Y, Huang Y, Liu Q. The First Transcriptome Assembly of Yenyuan Stream Salamander ( Batrachuperus yenyuanensis) Provides Novel Insights into Its Molecular Evolution. Int J Mol Sci 2019; 20:E1529. [PMID: 30934682 PMCID: PMC6480382 DOI: 10.3390/ijms20071529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/19/2022] Open
Abstract
The Yenyuan stream salamander (Batrachuperus yenyuanensis) has been previously evaluated with regards to phylogeny, population genetics, and hematology, but genomic information is sparse due to the giant genome size of salamanders which contain highly repetitive sequences, thus resulting in the lack of a complete reference genome. This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues. Using this transcriptome assembly and available encoding sequences from other vertebrates, the gene families, phylogenetic status, and species divergence time were compared or estimated. A total of 13,750 encoding sequences were successfully obtained from the transcriptome assembly of Yenyuan stream salamander, estimated to contain 40.1% of the unigenes represented in tetrapod databases. A total of 88.79% of these genes could be annotated to a biological function by current databases. Through gene family clustering, we found multiple possible isoforms of the Scribble gene-whose function is related to regeneration-based on sequence similarity. Meanwhile, we constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyuan stream salamander presents the closest relationship with the Chinese giant salamander (Andrias davidianus) of the investigated vertebrates. Based on the fossil-calibrated phylogeny, we estimated that the lineage divergence between the ancestral Yenyuan stream salamander and the Chinese giant salamander may have occurred during the Cretaceous period (~78.4 million years ago). In conclusion, this study not only provides a candidate gene that is valuable for exploring the remarkable capacity of regeneration in the future, but also gives an interesting insight into the understanding of Yenyuan stream salamander by this first transcriptome assembly.
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Affiliation(s)
- Jianli Xiong
- Laboratory of Adaptation and Evolution of Aquatic Animals, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
| | - Yunyun Lv
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Yong Huang
- Laboratory of Adaptation and Evolution of Aquatic Animals, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
| | - Qiangqiang Liu
- Laboratory of Adaptation and Evolution of Aquatic Animals, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
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15
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Cox AG, Tsomides A, Yimlamai D, Hwang KL, Miesfeld J, Galli GG, Fowl BH, Fort M, Ma KY, Sullivan MR, Hosios AM, Snay E, Yuan M, Brown KK, Lien EC, Chhangawala S, Steinhauser ML, Asara JM, Houvras Y, Link B, Vander Heiden MG, Camargo FD, Goessling W. Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth. EMBO J 2018; 37:embj.2018100294. [PMID: 30348863 DOI: 10.15252/embj.2018100294] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022] Open
Abstract
The Hippo pathway and its nuclear effector Yap regulate organ size and cancer formation. While many modulators of Hippo activity have been identified, little is known about the Yap target genes that mediate these growth effects. Here, we show that yap -/- mutant zebrafish exhibit defects in hepatic progenitor potential and liver growth due to impaired glucose transport and nucleotide biosynthesis. Transcriptomic and metabolomic analyses reveal that Yap regulates expression of glucose transporter glut1, causing decreased glucose uptake and use for nucleotide biosynthesis in yap -/- mutants, and impaired glucose tolerance in adults. Nucleotide supplementation improves Yap deficiency phenotypes, indicating functional importance of glucose-fueled nucleotide biosynthesis. Yap-regulated glut1 expression and glucose uptake are conserved in mammals, suggesting that stimulation of anabolic glucose metabolism is an evolutionarily conserved mechanism by which the Hippo pathway controls organ growth. Together, our results reveal a central role for Hippo signaling in glucose metabolic homeostasis.
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Affiliation(s)
- Andrew G Cox
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Allison Tsomides
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dean Yimlamai
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katie L Hwang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
| | | | - Giorgio G Galli
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brendan H Fowl
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Fort
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly Y Ma
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark R Sullivan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aaron M Hosios
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erin Snay
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Min Yuan
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kristin K Brown
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Evan C Lien
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sagar Chhangawala
- Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY, USA
| | - Matthew L Steinhauser
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John M Asara
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yariv Houvras
- Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY, USA
| | - Brian Link
- Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Fernando D Camargo
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Wolfram Goessling
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA .,Harvard Stem Cell Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
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16
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C2orf71a/pcare1 is important for photoreceptor outer segment morphogenesis and visual function in zebrafish. Sci Rep 2018; 8:9675. [PMID: 29946172 PMCID: PMC6018674 DOI: 10.1038/s41598-018-27928-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/17/2018] [Indexed: 02/03/2023] Open
Abstract
Mutations in C2orf71 are causative for autosomal recessive retinitis pigmentosa and occasionally cone-rod dystrophy. We have recently discovered that the protein encoded by this gene is important for modulation of the ciliary membrane through the recruitment of an actin assembly module, and have therefore renamed the gene to PCARE (photoreceptor cilium actin regulator). Here, we report on the identification of two copies of the c2orf71/pcare gene in zebrafish, pcare1 and pcare2. To study the role of the gene most similar to human PCARE, pcare1, we have generated a stable pcare1 mutant zebrafish model (designated pcare1rmc100/rmc100) in which the coding sequence was disrupted using CRISPR/Cas9 technology. Retinas of both embryonic (5 dpf) and adult (6 mpf) pcare1rmc100/rmc100 zebrafish display a clear disorganization of photoreceptor outer segments, resembling the phenotype observed in Pcare−/− mice. Optokinetic response and visual motor response measurements indicated visual impairment in pcare1rmc100/rmc100 zebrafish larvae at 5 dpf. In addition, electroretinogram measurements showed decreased b-wave amplitudes in pcare1rmc100/rmc100 zebrafish as compared to age- and strain-matched wild-type larvae, indicating a defect in the transretinal current. Altogether, our data show that lack of pcare1 causes a retinal phenotype in zebrafish and indicate that the function of the PCARE gene is conserved across species.
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17
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Hodgson P, Ireland J, Grunow B. Fish, the better model in human heart research? Zebrafish Heart aggregates as a 3D spontaneously cardiomyogenic in vitro model system. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 138:132-141. [PMID: 29729327 DOI: 10.1016/j.pbiomolbio.2018.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/04/2018] [Accepted: 04/27/2018] [Indexed: 12/25/2022]
Abstract
The zebrafish (ZF) has become an essential model for biomedical, pharmacological and eco-toxicological heart research. Despite the anatomical differences between fish and human hearts, similarities in cellular structure and conservation of genes as well as pathways across vertebrates have led to an increase in the popularity of ZF as a model for human cardiac research. ZF research benefits from an entirely sequenced genome, which allows us to establish and study cardiovascular mutants to better understand cardiovascular diseases. In this review, we will discuss the importance of in vitro model systems for cardiac research and summarise results of in vitro 3D heart-like cell aggregates, consisting of myocardial tissue formed spontaneously from enzymatically digested whole embryonic ZF larvae (Zebrafish Heart Aggregate - ZFHA). We will give an overview of the similarities and differences of ZF versus human hearts and highlight why ZF complement established mammalian models (i.e. murine and large animal models) for cardiac research. At this stage, the ZFHA model system is being refined into a high-throughput (more ZFHA generated than larvae prepared) and stable in vitro test system to accomplish the same longevity of previously successful salmonid models. ZFHA have potential for the use of high-throughput-screenings of different factors like small molecules, nucleic acids, proteins and lipids which is difficult to achieve in the zebrafish in vivo screening models with lethal mutations as well as to explore ion channel disorders and to find appropriate drugs for safety screening.
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Affiliation(s)
- Patricia Hodgson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK; Salford Royal NHS Foundation Trust, Stott Lane, Salford M6 8HD, UK
| | - Jake Ireland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK; School of Chemistry, Materials Science, and Engineering, Hilmer Building, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Bianka Grunow
- University Medicine Greifswald, Institute of Physiology, Greifswalder Str. 11C, 17495 Karlsburg, Germany; Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
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18
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Zhou X, Cao CY, Wan ATY, Yue GGL, Kwok FHF, Fung KP, Sun H, Lau CBS, Puno PT, Tsui SKW. Functional roles of eriocalyxin B in zebrafish revealed by transcriptome analysis. Mol Omics 2018; 14:156-169. [PMID: 29676772 DOI: 10.1039/c7mo00125h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eriocalyxin B (EriB) is a naturalent-kaurane diterpenoid obtained fromIsodon eriocalyxvar.laxiflora(family Lamiaceae), which exerted multiple biological activities (e.g.anti-tumor and anti-inflammatory)viathe alteration of gene expression and signaling transduction.
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Affiliation(s)
- Xunian Zhou
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
| | - Cyanne Ye Cao
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
| | - Grace Gar-Lee Yue
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
- China
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- The Chinese University of Hong Kong
| | - Frankie Hin-Fai Kwok
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
- China
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- The Chinese University of Hong Kong
| | - Kwok-Pui Fung
- School of Biomedical Sciences
- The Chinese University of Hong Kong
- China
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
| | - Handong Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- Kunming Institute of Botany
- Chinese Academy of Sciences
- Kunming 650201
- China
| | - Clara Bik-San Lau
- Institute of Chinese Medicine
- The Chinese University of Hong Kong
- China
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- The Chinese University of Hong Kong
| | - Pema-Tenzin Puno
- State Key Laboratory of Phytochemistry and Plant Resources in West China
- Kunming Institute of Botany
- Chinese Academy of Sciences
- Kunming 650201
- China
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19
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White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017; 6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022] Open
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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Affiliation(s)
| | - John E Collins
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Zsofia Digby
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Matthew P Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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20
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Ravasio V, Damiati E, Zizioli D, Orizio F, Giacopuzzi E, Manzoni M, Bresciani R, Borsani G, Monti E. Genomic and biochemical characterization of sialic acid acetylesterase (siae) in zebrafish. Glycobiology 2017; 27:938-946. [DOI: 10.1093/glycob/cwx068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/21/2017] [Indexed: 01/08/2023] Open
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21
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Transcriptional Complexity and Distinct Expression Patterns of auts2 Paralogs in Danio rerio. G3-GENES GENOMES GENETICS 2017. [PMID: 28626003 PMCID: PMC5555464 DOI: 10.1534/g3.117.042622] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Several genes that have been implicated in autism spectrum disorders (ASDs) have multiple transcripts. Therefore, comprehensive transcript annotation is critical for determining the respective gene function. The autism susceptibility candidate 2 (AUTS2) gene is associated with various neurological disorders, including autism and brain malformation. AUTS2 is important for activation of transcription of neural specific genes, neuronal migration, and neurite outgrowth. Here, we present evidence for significant transcriptional complexity in the auts2 gene locus in the zebrafish genome, as well as in genomic loci of auts2 paralogous genes fbrsl1 and fbrs. Several genes that have been implicated in ASDs are large and have multiple transcripts. Neurons are especially enriched with longer transcripts compared to nonneural cell types. The human autism susceptibility candidate 2 (AUTS2) gene is ∼1.2 Mb long and is implicated in a number of neurological disorders including autism, intellectual disability, addiction, and developmental delay. Recent studies show AUTS2 to be important for activation of transcription of neural specific genes, neuronal migration, and neurite outgrowth. However, much remains to be understood regarding the transcriptional complexity and the functional roles of AUTS2 in neurodevelopment. Zebrafish provide an excellent model system for studying both these questions. We undertook genomic identification and characterization of auts2 and its paralogous genes in zebrafish. There are four auts2 family genes in zebrafish: auts2a, auts2b, fbrsl1, and fbrs. The absence of complete annotation of their structures hampers functional studies. We present evidence for transcriptional complexity of these four genes mediated by alternative splicing and alternative promoter usage. Furthermore, the expression of the various paralogs is tightly regulated both spatially and developmentally. Our findings suggest that auts2 paralogs serve distinct functions in the development and functioning of target tissues.
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22
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Liu K, Xu D, Li J, Bian C, Duan J, Zhou Y, Zhang M, You X, You Y, Chen J, Yu H, Xu G, Fang DA, Qiang J, Jiang S, He J, Xu J, Shi Q, Zhang Z, Xu P. Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. Gigascience 2017; 6:1-6. [PMID: 28327943 PMCID: PMC5530312 DOI: 10.1093/gigascience/giw012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/13/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022] Open
Abstract
Background Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests. A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly. We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.
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Affiliation(s)
- Kai Liu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Dongpo Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
| | - Jinrong Duan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Yanfeng Zhou
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Minying Zhang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
| | - Yang You
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
| | - Hui Yu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
| | - Gangchun Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Di-an Fang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Jun Qiang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Shulun Jiang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Jie He
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
- BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, Guangdong 518083, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, Guangdong 518083, China
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
- BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, Guangdong 518083, China
- Laboratory of Aquatic Genomics, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Zhiyong Zhang
- Institute of Oceanology & Marine Fisheries, Nantong, Jiangsu 226007, China
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
- BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, Guangdong 518083, China
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23
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Anelli V, Villefranc JA, Chhangawala S, Martinez-McFaline R, Riva E, Nguyen A, Verma A, Bareja R, Chen Z, Scognamiglio T, Elemento O, Houvras Y. Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression. eLife 2017; 6. [PMID: 28350298 PMCID: PMC5389860 DOI: 10.7554/elife.20728] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Thyroid cancer is common, yet the sequence of alterations that promote tumor formation are incompletely understood. Here, we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real-time in vivo imaging, we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease-free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue, we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E-mediated transformation. DOI:http://dx.doi.org/10.7554/eLife.20728.001
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Affiliation(s)
- Viviana Anelli
- Department of Surgery, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
| | - Jacques A Villefranc
- Department of Surgery, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
| | - Sagar Chhangawala
- Department of Surgery, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
| | - Raul Martinez-McFaline
- Department of Surgery, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
| | - Eleonora Riva
- Section of Endocrinology, Department of Medical Science, University of Ferrara, Ferrara, Italy
| | - Anvy Nguyen
- Department of Surgery, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
| | - Akanksha Verma
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York City, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, United States
| | - Rohan Bareja
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York City, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, United States
| | - Zhengming Chen
- Department of Healthcare Policy & Research, Weill Cornell Medical College, New York City, United States
| | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York City, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, United States
| | - Yariv Houvras
- Department of Surgery, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States.,Department of Medicine, Weill Cornell Medical College, New York Presbyterian Hospital, New York City, United States
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24
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Abstract
Gene finding is the process of identifying genome sequence regions representing stretches of DNA that encode biologically active products, such as proteins or functional noncoding RNAs. As this is usually the first step in the analysis of any novel genomic sequence or resequenced sample of well-known organisms, it is a very important issue, as all downstream analyses depend on the results. This chapter describes the biological basis for gene finding, and the programs and computational approaches that are available for the automated identification of protein-coding genes. For bacterial, archaeal, and eukaryotic genomes, as well as for multi-species sequence data originating from environmental community studies, the state of the art in automated gene finding is described.
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Affiliation(s)
- Alice Carolyn McHardy
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany.
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany.
| | - Andreas Kloetgen
- Department for Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany
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25
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Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Database (Oxford) 2017; 2017:3074789. [PMID: 28365736 PMCID: PMC5467575 DOI: 10.1093/database/bax020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/07/2017] [Accepted: 02/20/2017] [Indexed: 01/09/2023]
Abstract
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). Database URL http://www.ensembl.org.
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Affiliation(s)
- Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas Kähäri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monika Komorowska
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Keenan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Longden
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Glenn Proctor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steve Searle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kieron Taylor
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alessandro Vullo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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26
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Yang L, Zhang Z, He S. Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes. Genome Biol Evol 2016; 8:3433-3445. [PMID: 27742722 PMCID: PMC5203780 DOI: 10.1093/gbe/evw239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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27
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Snake Genome Sequencing: Results and Future Prospects. Toxins (Basel) 2016; 8:toxins8120360. [PMID: 27916957 PMCID: PMC5198554 DOI: 10.3390/toxins8120360] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 12/16/2022] Open
Abstract
Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.
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28
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Down-regulation of coasy, the gene associated with NBIA-VI, reduces Bmp signaling, perturbs dorso-ventral patterning and alters neuronal development in zebrafish. Sci Rep 2016; 6:37660. [PMID: 27892483 PMCID: PMC5124858 DOI: 10.1038/srep37660] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/01/2016] [Indexed: 12/16/2022] Open
Abstract
Mutations in Pantothenate kinase 2 and Coenzyme A (CoA) synthase (COASY), genes involved in CoA biosynthesis, are associated with rare neurodegenerative disorders with brain iron accumulation. We showed that zebrafish pank2 gene plays an essential role in brain and vasculature development. Now we extended our study to coasy. The gene has high level of sequence identity with the human ortholog and is ubiquitously expressed from the earliest stages of development. The abrogation of its expression led to strong reduction of CoA content, high lethality and a phenotype resembling to that of dorsalized mutants. Lower doses of morpholino resulted in a milder phenotype, with evident perturbation in neurogenesis and formation of vascular arborization; the dorso-ventral patterning was severely affected, the expression of bone morphogenetic protein (Bmp) receptors and activity were decreased, while cell death increased. These features specifically correlated with the block in CoA biosynthesis and were rescued by the addition of CoA to fish water and the overexpression of the human wild-type, but not mutant gene. These results confirm the absolute requirement for adequate levels of CoA for proper neural and vascular development in zebrafish and point to the Bmp pathway as a possible molecular connection underlining the observed phenotype.
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29
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Kazokaitė J, Aspatwar A, Kairys V, Parkkila S, Matulis D. Fluorinated benzenesulfonamide anticancer inhibitors of carbonic anhydrase IX exhibit lower toxic effects on zebrafish embryonic development than ethoxzolamide. Drug Chem Toxicol 2016; 40:309-319. [PMID: 27600313 DOI: 10.1080/01480545.2016.1223095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The toxic effects of two recently discovered inhibitors (VD12-09 and VD11-4-2) that selectively and with extraordinary strong, picomolar binding affinity to human carbonic anhydrase (CA) isoform IX were investigated on zebrafish embryonic development. CA IX has been recently introduced as an anticancer target since it is highly overexpressed in numerous human cancers but nearly absent in normal tissues. Morphological changes in zebrafish treated by the compounds were studied by light-field microscopy and histological analysis. Homology models of zebrafish CA II and CA IX were built to identify the conserved amino acid residues in the active site of zebrafish CAs. The toxicity studies here showed that the LC50 values at 120 hours post-fertilization (hpf) were 13 μM for VD12-09, 120 μM for VD11-4-2, and 9 μM for ethoxzolamide (EZA), a non-selective CA inhibitor commonly used as a drug in clinics. Thus, EZA was the most toxic of the three compounds. The zebrafish embryos exposed to LC50 doses of VD12-09 and VD11-4-2 showed fewer phenotypic abnormalities compared with the embryos exposed to the corresponding dose of EZA. Histochemical studies did not show any gross morphological changes in the embryos treated with VD12-09 and VD11-4-2 unlike EZA. The results of our study indicate that the compounds exhibited 10-fold lower toxicity and induced fewer side effects in zebrafish than EZA. Therefore, the exposure to VD11-4-2 and VD12-09 at concentrations below LC50 did not lead to deleterious effects on the zebrafish embryonic development and thus both inhibitors may be further developed as drugs.
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Affiliation(s)
- Justina Kazokaitė
- a Department of Biothermodynamics and Drug Design , Institute of Biotechnology, Vilnius University , Vilnius , Lithuania
| | - Ashok Aspatwar
- b Faculty of Medicine and Life Sciences , University of Tampere , Tampere , Finland.,c Fimlab Ltd, Tampere University Hospital , Tampere , Finland , and
| | - Visvaldas Kairys
- d Department of Bioinformatics , Institute of Biotechnology, Vilnius University , Vilnius , Lithuania
| | - Seppo Parkkila
- b Faculty of Medicine and Life Sciences , University of Tampere , Tampere , Finland.,c Fimlab Ltd, Tampere University Hospital , Tampere , Finland , and
| | - Daumantas Matulis
- a Department of Biothermodynamics and Drug Design , Institute of Biotechnology, Vilnius University , Vilnius , Lithuania
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30
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Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis. Proc Natl Acad Sci U S A 2016; 113:E5562-71. [PMID: 27588899 DOI: 10.1073/pnas.1600204113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Selenium, an essential micronutrient known for its cancer prevention properties, is incorporated into a class of selenocysteine-containing proteins (selenoproteins). Selenoprotein H (SepH) is a recently identified nucleolar oxidoreductase whose function is not well understood. Here we report that seph is an essential gene regulating organ development in zebrafish. Metabolite profiling by targeted LC-MS/MS demonstrated that SepH deficiency impairs redox balance by reducing the levels of ascorbate and methionine, while increasing methionine sulfoxide. Transcriptome analysis revealed that SepH deficiency induces an inflammatory response and activates the p53 pathway. Consequently, loss of seph renders larvae susceptible to oxidative stress and DNA damage. Finally, we demonstrate that seph interacts with p53 deficiency in adulthood to accelerate gastrointestinal tumor development. Overall, our findings establish that seph regulates redox homeostasis and suppresses DNA damage. We hypothesize that SepH deficiency may contribute to the increased cancer risk observed in cohorts with low selenium levels.
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31
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Abernathy J, Overturf K. Comparison of Ribosomal RNA Removal Methods for Transcriptome Sequencing Workflows in Teleost Fish. Anim Biotechnol 2016; 27:60-5. [PMID: 26732342 DOI: 10.1080/10495398.2015.1086365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
RNA sequencing (RNA-Seq) is becoming the standard for transcriptome analysis. Removal of contaminating ribosomal RNA (rRNA) is a priority in the preparation of libraries suitable for sequencing. These methods have been well documented in mammals but typically require some optimization for lower vertebrates. Three commercial kits, including Dynabeads mRNA Purification Kit, RiboMinus Eukaryote System v2, and Ribo-Zero Gold rRNA Removal Kit were examined for the ability to remove rRNAs from rainbow trout (Oncorhynchus mykiss) RNA isolations. Total RNA was isolated from liver and muscle tissue samples (n = 24) and rRNAs removed using one of the three kits. Samples were analyzed visually on the Agilent Bioanalyzer and by Illumina RNA-seq, screening for Oncorhynchus rRNAs. There were significant differences between the kits in regards to their ability to remove rRNA, ranging from 2.74% - 10.94% rRNA sequences left behind per kit on average. Using the Bioanalyzer to evaluate ribosomal contamination in rRNA-depleted samples for RNA-Seq was good for detecting samples with higher concentrations of rRNA (>5%), but not very accurate at lower levels. Although all three kits were able to remove a substantial portion of the rRNA from different fish tissues, the Ribo-Zero Gold rRNA Removal Kit eliminated significantly more contaminating ribosomal RNAs than the others.
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Affiliation(s)
- Jason Abernathy
- a USDA-ARS , Hagerman Fish Culture Experiment Station , Hagerman , Idaho , USA
| | - Ken Overturf
- a USDA-ARS , Hagerman Fish Culture Experiment Station , Hagerman , Idaho , USA
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Yap reprograms glutamine metabolism to increase nucleotide biosynthesis and enable liver growth. Nat Cell Biol 2016; 18:886-896. [PMID: 27428308 PMCID: PMC4990146 DOI: 10.1038/ncb3389] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 06/16/2016] [Indexed: 02/06/2023]
Abstract
The Hippo pathway is an important regulator of organ size and tumorigenesis. It is unclear, however, how Hippo signaling provides the cellular building blocks required for rapid growth. Here, we demonstrate that transgenic zebrafish expressing an activated form of the Hippo pathway effector Yap1 (also known as YAP) develop enlarged livers and are prone to liver tumor formation. Transcriptomic and metabolomic profiling identify that Yap1 reprograms glutamine metabolism. Yap1 directly enhances glutamine synthetase (glul) expression and activity, elevating steady-state levels of glutamine and enhancing the relative isotopic enrichment of nitrogen during de novo purine and pyrimidine biosynthesis. Genetic or pharmacological inhibition of GLUL diminishes the isotopic enrichment of nitrogen into nucleotides, suppresses hepatomegaly and the growth of liver cancer cells. Consequently, Yap-driven liver growth is susceptible to nucleotide inhibition. Together, our findings demonstrate that Yap1 integrates the anabolic demands of tissue growth during development and tumorigenesis by reprogramming nitrogen metabolism to stimulate nucleotide biosynthesis.
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Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD, Ketting RF. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol 2016; 17:146. [PMID: 27381023 PMCID: PMC4934011 DOI: 10.1186/s13059-016-1013-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/20/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Enhancers, not promoters, are the most dynamic in their DNA methylation status throughout development and differentiation. Generally speaking, enhancers that are primed to or actually drive gene expression are characterized by relatively low levels of DNA methylation (hypo-methylation), while inactive enhancers display hyper-methylation of the underlying DNA. The direct functional significance of the DNA methylation state of enhancers is, however, unclear for most loci. RESULTS In contrast to conventional epigenetic interactions at enhancers, we find that DNA methylation status and enhancer activity during early zebrafish development display very unusual correlation characteristics: hypo-methylation is a unique feature of primed enhancers whereas active enhancers are generally hyper-methylated. The hypo-methylated enhancers that we identify (hypo-enhancers) are enriched close to important transcription factors that act later in development. Interestingly, hypo-enhancers are de-methylated shortly before the midblastula transition and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers do become active at later developmental stages and that they are physically associated with the transcriptional start site of target genes, irrespective of target gene activity. CONCLUSIONS We demonstrate that early development in zebrafish embodies a time window characterized by non-canonical DNA methylation-enhancer relationships, including global DNA hypo-methylation of inactive enhancers and DNA hyper-methylation of active enhancers.
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Affiliation(s)
- Lucas J T Kaaij
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, 3508 AB, Utrecht, The Netherlands
| | - Meng Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael Musheev
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | - Geert Geeven
- Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Adrien S J Melquiond
- Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | | | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, D-69120, Heidelberg, Germany
| | - Andrew D Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - René F Ketting
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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34
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Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SMJ. The Ensembl gene annotation system. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw093. [PMID: 27337980 PMCID: PMC4919035 DOI: 10.1093/database/baw093] [Citation(s) in RCA: 654] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/12/2022]
Abstract
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.
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Affiliation(s)
- Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah Ayling
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Present addresses: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Laura Clarke
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Valery Curwen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julio Fernandez Banet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Pfizer Inc, 10646 Science Center Dr, San Diego, CA 92121, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kevin Howe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas Kähäri
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Institutionen för cell-och molekylärbiologi, Uppsala University, Husargatan 3, Uppsala 752 37, Sweden
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Magali Ruffier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Schuster
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna a-1090, Austria
| | - Y Amy Tang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amonida Zadissa
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Genge CE, Lin E, Lee L, Sheng X, Rayani K, Gunawan M, Stevens CM, Li AY, Talab SS, Claydon TW, Hove-Madsen L, Tibbits GF. The Zebrafish Heart as a Model of Mammalian Cardiac Function. Rev Physiol Biochem Pharmacol 2016; 171:99-136. [PMID: 27538987 DOI: 10.1007/112_2016_5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Zebrafish (Danio rerio) are widely used as vertebrate model in developmental genetics and functional genomics as well as in cardiac structure-function studies. The zebrafish heart has been increasingly used as a model of human cardiac function, in part, due to the similarities in heart rate and action potential duration and morphology with respect to humans. The teleostian zebrafish is in many ways a compelling model of human cardiac function due to the clarity afforded by its ease of genetic manipulation, the wealth of developmental biological information, and inherent suitability to a variety of experimental techniques. However, in addition to the numerous advantages of the zebrafish system are also caveats related to gene duplication (resulting in paralogs not present in human or other mammals) and fundamental differences in how zebrafish hearts function. In this review, we discuss the use of zebrafish as a cardiac function model through the use of techniques such as echocardiography, optical mapping, electrocardiography, molecular investigations of excitation-contraction coupling, and their physiological implications relative to that of the human heart. While some of these techniques (e.g., echocardiography) are particularly challenging in the zebrafish because of diminutive size of the heart (~1.5 mm in diameter) critical information can be derived from these approaches and are discussed in detail in this article.
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Affiliation(s)
- Christine E Genge
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Eric Lin
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Ling Lee
- BC Children's Hospital Research Institute, Vancouver, BC, Canada, V5Z 4H4
| | - XiaoYe Sheng
- BC Children's Hospital Research Institute, Vancouver, BC, Canada, V5Z 4H4
| | - Kaveh Rayani
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Marvin Gunawan
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Charles M Stevens
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6.,BC Children's Hospital Research Institute, Vancouver, BC, Canada, V5Z 4H4
| | - Alison Yueh Li
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Sanam Shafaat Talab
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Thomas W Claydon
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Leif Hove-Madsen
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6.,Cardiovascular Research Centre CSIC-ICCC, Hospital de Sant Pau, Barcelona, Spain
| | - Glen F Tibbits
- Molecular Cardiac Physiology Group, Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6. .,BC Children's Hospital Research Institute, Vancouver, BC, Canada, V5Z 4H4.
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36
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Daly C, Yin J, Kennedy BN. Histone Deacetylase: Therapeutic Targets in Retinal Degeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 854:455-61. [PMID: 26427446 DOI: 10.1007/978-3-319-17121-0_61] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Previous studies report that retinitis pigmentosa (RP) patients treated with the histone deacetylase inhibitor (HDACi) valproic acid (VPA) present with improved visual fields and delayed vision loss. However, other studies report poor efficacy and safety of HDACi in other cohorts of retinal degeneration patients. Furthermore, the molecular mechanisms by which HDACi can improve visual function is unknown, albeit HDACi can attenuate pro-apoptotic stimuli and induce expression of neuroprotective factors. Thus, further analysis of HDACi is warranted in pre-clinical models of retinal degeneration including zebrafish. Analysis of HDAC expression in developing zebrafish reveals diverse temporal expression patterns during development and maturation of visual function.
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Affiliation(s)
- Conor Daly
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, 4, Dublin, Ireland.
| | - Jun Yin
- Department of Genetics, Yale University School of Medicine, 06520, New Haven, CT, USA.
| | - Breandán N Kennedy
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, 4, Dublin, Ireland.
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37
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Zhong Z, Yang L, Zhang YE, Xue Y, He S. Correlated expression of retrocopies and parental genes in zebrafish. Mol Genet Genomics 2015; 291:723-37. [PMID: 26561303 DOI: 10.1007/s00438-015-1140-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/27/2015] [Indexed: 12/15/2022]
Abstract
Previous studies of the function and evolution of retrocopies in plants, Drosophila and non-mammalian chordates provided new insights into the origin of novel genes. However, little is known about retrocopies and their parental genes in teleosts, and it remains obscure whether there is any correlation between them. The present study aimed to characterize the spatial and temporal expression profiles of retrogenes and their parental genes based on RNA-Seq data from Danio rerio embryos and tissues from adult. Using a modified pipeline, 306 retrocopies were identified in the zebrafish genome, most of which exhibited ancient retroposition, and 76 of these showed a Ks < 2.0. Expression of a retrocopy is generally expected to present no correlation with its parental gene, as regulatory regions are not part of the retroposition event. Here, this assumption was tested based on RNA-Seq data from eight stages and thirteen tissue types of zebrafish. However, the result suggested that retrocopies displayed correlated expression with their parental genes. The level of correlation was found to decrease during embryogenesis, but to increase slightly within a tissue using Ks as the proxy for the divergence time. Tissue specificity was also observed: retrocopies were found to be expressed at a more specific level compared with their parental genes. Unlike Drosophila, which has sex chromosomes, zebrafish do not show testis-biased expression. Our study elaborated temporal and spatial patterns of expression of retrocopies in zebrafish, examined the correlation between retrocopies and parental genes and analyzed potential source of regulated elements of retrocopies, which lay a foundation for further functional study of retrocopies.
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Affiliation(s)
- Zaixuan Zhong
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yong E Zhang
- Key Laboratory of the Zoological Systematic and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Beijing, 100000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yu Xue
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, People's Republic of China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, People's Republic of China.
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38
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Collins JE, Wali N, Sealy IM, Morris JA, White RJ, Leonard SR, Jackson DK, Jones MC, Smerdon NC, Zamora J, Dooley CM, Carruthers SN, Barrett JC, Stemple DL, Busch-Nentwich EM. High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping. BMC Genomics 2015; 16:578. [PMID: 26238335 PMCID: PMC4524448 DOI: 10.1186/s12864-015-1788-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. RESULTS Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. CONCLUSIONS This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.
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Affiliation(s)
- John E Collins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Neha Wali
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - James A Morris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Richard J White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Steven R Leonard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - David K Jackson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Matthew C Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nathalie C Smerdon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jorge Zamora
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Christopher M Dooley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Samantha N Carruthers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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Deml B, Reis LM, Muheisen S, Bick D, Semina EV. EFTUD2 deficiency in vertebrates: Identification of a novel human mutation and generation of a zebrafish model. ACTA ACUST UNITED AC 2015; 103:630-40. [PMID: 26118977 DOI: 10.1002/bdra.23397] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/30/2015] [Accepted: 05/26/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Congenital microphthalmia and coloboma are severe developmental defects that are frequently associated with additional systemic anomalies and display a high level of genetic heterogeneity. METHODS To identify the pathogenic variant in a patient with microphthalmia, coloboma, retinal dystrophy, microcephaly, and other features, whole exome sequencing analysis of the patient and parental samples was undertaken. To further explore the identified variant/gene, expression and functional studies in zebrafish were performed. RESULTS Whole exome sequencing revealed a de novo variant, c.473_474delGA, p.(Arg158Lysfs*4), in EFTUD2 which encodes a component of the spliceosome complex. Dominant mutations in EFTUD2 cause Mandibulofacial Dysostosis, Guion-Almeida type, which does not involve microphthalmia, coloboma, or retinal dystrophy; analysis of genes known to cause these ocular phenotypes identified several variants of unknown significance but no causal alleles in the affected patient. Zebrafish eftud2 demonstrated high sequence conservation with the human gene and broad embryonic expression. TALEN-mediated disruption was employed to generate a c.378_385 del, p.(Ser127Aspfs*23) truncation mutation in eftud2. Homozygous mutants displayed a reduced head size, small eye, curved body, and early embryonic lethality. Apoptosis assays demonstrated a striking increase in terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL)-positive cells in the developing brain, eye, spinal cord, and other tissues starting at 30 hours postfertilization. CONCLUSION This study reports a novel mutation in EFTUD2 in a Mandibulofacial Dysostosis, Guion-Almeida type patient with unusual ocular features and the generation of a first animal model of eftud2 deficiency. The severe embryonic phenotype observed in eftud2 mutants indicates an important conserved role during development of diverse tissues in vertebrates.
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Affiliation(s)
- Brett Deml
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - David Bick
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
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40
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He L, Pei Y, Jiang Y, Li Y, Liao L, Zhu Z, Wang Y. Global gene expression patterns of grass carp following compensatory growth. BMC Genomics 2015; 16:184. [PMID: 25887225 PMCID: PMC4374334 DOI: 10.1186/s12864-015-1427-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome. Most animals, especially fish, are capable of compensatory growth, but the mechanisms remain unclear. Further investigation of the mechanism of compensatory growth in fish is needed to improve feeding efficiency, reduce cost, and explore growth-related genes. RESULTS In the study, grass carp, an important farmed fish in China, were subjected to a compensatory growth experiment followed by transcriptome analysis by RNA-sequencing. Samples of fish from starved and re-feeding conditions were compared with the control. Under starved conditions, 4061 and 1988 differentially expressed genes (DEGs) were detected in muscle and liver tissue when compared the experimental group with control group, respectively. After re-feeding, 349 and 247 DEGs were identified in muscle and liver when the two groups were compared. Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver. Most of these DEGs were involved in metabolic processes, or encoded enzymes or proteins with catalytic activity or binding functions, or involved in metabolic and biosynthetic pathways. A number of the more significant DEGs were subjected to further analysis. Under fasting conditions, many up-regulated genes were associated with protein ubiquitination or degradation, whereas many down-regulated genes were involved in the metabolism of glucose and fatty acids. Under re-feeding conditions, genes participating in muscle synthesis and fatty acid metabolism were up-regulated significantly, and genes related to protein ubiquitination or degradation were down-regulated. Moreover, Several DEGs were random selected for confirmation by real-time quantitative PCR. CONCLUSIONS Global gene expression patterns of grass carp during compensatory growth were determined. To our knowledge, this is a first reported for a teleost fish. The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.
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Affiliation(s)
- Libo He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yongyan Pei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yao Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Zhang X, Wang S, Chen S, Chen Y, Liu Y, Shao C, Wang Q, Lu Y, Gong G, Ding S, Sha Z. Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2015; 43:209-218. [PMID: 25543033 DOI: 10.1016/j.fsi.2014.11.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/15/2014] [Accepted: 11/16/2014] [Indexed: 06/04/2023]
Abstract
Half-smooth tongue sole (Cynoglossus semilaevis) is one of the most valuable marine aquatic species in Northern China. Given to the rapid development of aquaculture industry, the C. semilaevis was subjected to disease-causing bacteria Vibrio anguillarum. It therefore is indispensable and urgent to understand the mechanism of C. semilaevis host defense against V. anguillarum infection. In the present study, the extensively analysis at the transcriptome level for V. Anguillarum disease in tongue sole was carried out. In total, 94,716 high quality contigs were generated from 75,884,572 clean reads in three libraries (HOSG, NOSG, and CG). 22,746 unigenes were identified when compared with SwissProt, an NR protein database and NT nucleotide database. 954 genes exhibiting the differentially expression at least one pair of comparison in all three libraries were identified. GO enrichment for these genes revealed gene response to biotic stimulus, immune system regulation, and immune response and cytokine production. Further, the pathways such as complement and coagulation cascades and Vibrio cholerae infection pathways were enriched in defensing of pathogen. Besides, 13,428 SSRs and 118,239 SNPs were detected in tongue sole, providing further support for genetic variation and marker-assisted selection in future. In summary, this study identifies several putative immune pathways and candidate genes deserving further investigation in the context of development of therapeutic regimens and lays the foundation for selecting resistant lines of C. semilaevis against V. anguillarum.
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Affiliation(s)
- Xiang Zhang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China; Laboratory of Marine Biodiversity and Global Change, College of Oceanography and Environmental Science, Xiamen University, 182 Daxue Road, Xiamen 361005, Fujian, China
| | - Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, 1670 Discovery Drive, Suite 110, Charlottesville 22911, VA, USA
| | - Songlin Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yadong Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yang Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Changwei Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Qilong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yang Lu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Guangye Gong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Shaoxiong Ding
- Laboratory of Marine Biodiversity and Global Change, College of Oceanography and Environmental Science, Xiamen University, 182 Daxue Road, Xiamen 361005, Fujian, China
| | - Zhenxia Sha
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China.
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Harty BL, Krishnan A, Sanchez NE, Schiöth HB, Monk KR. Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish. BMC Genomics 2015; 16:62. [PMID: 25715737 PMCID: PMC4335454 DOI: 10.1186/s12864-015-1296-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/29/2015] [Indexed: 01/03/2023] Open
Abstract
Background Adhesion G protein-coupled receptors (aGPCRs) are the second largest of the five GPCR families and are essential for a wide variety of physiological processes. Zebrafish have proven to be a very effective model for studying the biological functions of aGPCRs in both developmental and adult contexts. However, aGPCR repertoires have not been defined in any fish species, nor are aGPCR expression profiles in adult tissues known. Additionally, the expression profiles of the aGPCR family have never been extensively characterized over a developmental time-course in any species. Results Here, we report that there are at least 59 aGPCRs in zebrafish that represent homologs of 24 of the 33 aGPCRs found in humans; compared to humans, zebrafish lack clear homologs of GPR110, GPR111, GPR114, GPR115, GPR116, EMR1, EMR2, EMR3, and EMR4. We find that several aGPCRs in zebrafish have multiple paralogs, in line with the teleost-specific genome duplication. Phylogenetic analysis suggests that most zebrafish aGPCRs cluster closely with their mammalian homologs, with the exception of three zebrafish-specific expansion events in Groups II, VI, and VIII. Using quantitative real-time PCR, we have defined the expression profiles of 59 zebrafish aGPCRs at 12 developmental time points and 10 adult tissues representing every major organ system. Importantly, expression profiles of zebrafish aGPCRs in adult tissues are similar to those previously reported in mouse, rat, and human, underscoring the evolutionary conservation of this family, and therefore the utility of the zebrafish for studying aGPCR biology. Conclusions Our results support the notion that zebrafish are a potentially useful model to study the biology of aGPCRs from a functional perspective. The zebrafish aGPCR repertoire, classification, and nomenclature, together with their expression profiles during development and in adult tissues, provides a crucial foundation for elucidating aGPCR functions and pursuing aGPCRs as therapeutic targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1296-8) contains supplementary material, which is available to authorized users.
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Hypothalamic differences in expression of genes involved in monoamine synthesis and signaling pathways after insulin injection in chickens from lines selected for high and low body weight. Neurogenetics 2015; 16:133-44. [PMID: 25582322 DOI: 10.1007/s10048-014-0435-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
Abstract
Long-term selection for juvenile body weight from a common founder population resulted in two divergent chicken lines (low-weight selected line (LWS), high-weight selected line (HWS)) that display distinct food intake and blood glucose responses to exogenous neuropeptides and insulin. The objective of this study was to elucidate putative targets affecting food intake and energy homeostasis by sequencing hypothalamic RNA from LWS and HWS chickens after insulin injection. Ninety-day-old female LWS and HWS chickens were injected with either vehicle or insulin and hypothalamus collected at 1 h postinjection. Through RNA sequencing, a total of 361 differentially expressed genes (DEGs) were identified. There was greater expression of genes, mainly tyrosine hydroxylase (TH), L-aromatic amino acid decarboxylase (DDC), and vesicular monoamine transporter (VMAT), involved in serotonin and dopamine biosynthesis and signaling in LWS than in HWS vehicle-injected chickens. In contrast, after insulin injection, these genes were more highly expressed in HWS than in LWS. We identified 90 single nucleotide polymorphisms (SNPs) existing only in the HWS and 121 SNPs specific to LWS and 5119 SNPs close to fixation (with absolute frequency difference ≥0.9). Four were located in genes encoding enzymes associated with serotonergic and dopaminergic pathways, such as DDC, TH, and solute carrier family 18, member 2 (VMAT). These data implicate differences in biogenic amines such as serotonin and dopamine in hypothalamic physiology between the chicken lines, and these differences might be associated with polymorphisms during long-term selection. Changes in serotonergic and dopaminergic signaling pathways in response to insulin injection suggest a role in whole-body energy homeostasis.
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44
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Benzekri H, Armesto P, Cousin X, Rovira M, Crespo D, Merlo MA, Mazurais D, Bautista R, Guerrero-Fernández D, Fernandez-Pozo N, Ponce M, Infante C, Zambonino JL, Nidelet S, Gut M, Rebordinos L, Planas JV, Bégout ML, Claros MG, Manchado M. De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray. BMC Genomics 2014; 15:952. [PMID: 25366320 PMCID: PMC4232633 DOI: 10.1186/1471-2164-15-952] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 10/15/2014] [Indexed: 12/26/2022] Open
Abstract
Background Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution. Results A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB. Conclusions Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-952) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Manuel Manchado
- IFAPA Centro El Toruño, IFAPA, Consejeria de Agricultura y Pesca, 11500 El Puerto de Santa María, Cádiz, Spain.
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45
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Yin J, Morrissey ME, Shine L, Kennedy C, Higgins DG, Kennedy BN. Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis. BMC Genomics 2014; 15:825. [PMID: 25266257 PMCID: PMC4190348 DOI: 10.1186/1471-2164-15-825] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 09/24/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The genetic cascades underpinning vertebrate early eye morphogenesis are poorly understood. One gene family essential for eye morphogenesis encodes the retinal homeobox (Rx) transcription factors. Mutations in the human retinal homeobox gene (RAX) can lead to gross morphological phenotypes ranging from microphthalmia to anophthalmia. Zebrafish rx3 null mutants produce a similar striking eyeless phenotype with an associated expanded forebrain. Thus, we used zebrafish rx3-/- mutants as a model to uncover an Rx3-regulated gene network during early eye morphogenesis. RESULTS Rx3-regulated genes were identified using whole transcriptomic sequencing (RNA-seq) of rx3-/- mutants and morphologically wild-type siblings during optic vesicle morphogenesis. A gene co-expression network was then constructed for the Rx3-regulated genes, identifying gene cross-talk during early eye development. Genes highly connected in the network are hub genes, which tend to exhibit higher expression changes between rx3-/- mutants and normal phenotype siblings. Hub genes down-regulated in rx3-/- mutants encompass homeodomain transcription factors and mediators of retinoid-signaling, both associated with eye development and known human eye disorders. In contrast, genes up-regulated in rx3-/- mutants are centered on Wnt signaling pathways, associated with brain development and disorders. The temporal expression pattern of Rx3-regulated genes was further profiled during early development from maternal stage until visual function is fully mature. Rx3-regulated genes exhibited synchronized expression patterns, and a transition of gene expression during the early segmentation stage when Rx3 was highly expressed. Furthermore, most of these deregulated genes are enriched with multiple RAX-binding motif sequences on the gene promoter. CONCLUSIONS Here, we assembled a comprehensive model of Rx3-regulated genes during early eye morphogenesis. Rx3 promotes optic vesicle morphogenesis and represses brain development through a highly correlated and modulated network, exhibiting repression of genes mediating Wnt signaling and concomitant enhanced expression of homeodomain transcription factors and retinoid-signaling genes.
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Affiliation(s)
- Jun Yin
- />UCD Conway Institute, UCD School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4 Ireland
- />Department of Genetics, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Maria E Morrissey
- />UCD Conway Institute, UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4 Ireland
| | - Lisa Shine
- />UCD Conway Institute, UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4 Ireland
| | - Ciarán Kennedy
- />UCD Conway Institute, UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4 Ireland
| | - Desmond G Higgins
- />UCD Conway Institute, UCD School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4 Ireland
| | - Breandán N Kennedy
- />UCD Conway Institute, UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4 Ireland
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46
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Alli Shaik A, Wee S, Li RHX, Li Z, Carney TJ, Mathavan S, Gunaratne J. Functional Mapping of the Zebrafish Early Embryo Proteome and Transcriptome. J Proteome Res 2014; 13:5536-50. [DOI: 10.1021/pr5005136] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Asfa Alli Shaik
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Sheena Wee
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Rachel Hai Xia Li
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Zhen Li
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Tom J. Carney
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
| | - Sinnakaruppan Mathavan
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Jayantha Gunaratne
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
- Department
of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore
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47
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Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. Diversity and dynamics of the Drosophila transcriptome. Nature 2014; 512:393-9. [PMID: 24670639 PMCID: PMC4152413 DOI: 10.1038/nature12962] [Citation(s) in RCA: 470] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 12/18/2013] [Indexed: 01/10/2023]
Abstract
Animal transcriptomes are dynamic, with each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. Here we have identified new genes, transcripts and proteins using poly(A)+ RNA sequencing from Drosophila melanogaster in cultured cell lines, dissected organ systems and under environmental perturbations. We found that a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites.
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48
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Sumbre G, de Polavieja GG. The world according to zebrafish: how neural circuits generate behavior. Front Neural Circuits 2014; 8:91. [PMID: 25126059 PMCID: PMC4115616 DOI: 10.3389/fncir.2014.00091] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/11/2014] [Indexed: 11/17/2022] Open
Affiliation(s)
- Germán Sumbre
- Ecole Normale Supérieure, Institut de Biologie de l'ENS Paris, France ; Inserm, U1024 Paris, France ; CNRS, UMR 8197 Paris, France
| | - Gonzalo G de Polavieja
- Instituto Cajal, Consejo Superior de Investigaciones Científicas Madrid, Spain ; Champalimaud Neuroscience Programme, Champalimaud Center for the Unknown Lisbon, Portugal
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49
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Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LDN, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TSK, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics 2014; 13:3184-98. [PMID: 25060758 DOI: 10.1074/mcp.m114.038299] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes.
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Affiliation(s)
- Dhanashree S Kelkar
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Elayne Provost
- §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205
| | - Raghothama Chaerkady
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Babylakshmi Muthusamy
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Srikanth S Manda
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Tejaswini Subbannayya
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Lakshmi Dhevi N Selvan
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Chieh-Huei Wang
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Keshava K Datta
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡‡School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Sunghee Woo
- §§Department of Computer Science, University of California, San Diego, California 92093
| | - Sutopa B Dwivedi
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Santosh Renuse
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Derese Getnet
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Tai-Chung Huang
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Min-Sik Kim
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sneha M Pinto
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Christopher J Mitchell
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Anil K Madugundu
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Praveen Kumar
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Jyoti Sharma
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Jayshree Advani
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Gourav Dey
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Lavanya Balakrishnan
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖‖Department of Biotechnology, Kuvempu University, Shimoga 577 451, India
| | - Nazia Syed
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Vishalakshi Nanjappa
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Yashwanth Subbannayya
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Renu Goel
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - T S Keshava Prasad
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Vineet Bafna
- §§Department of Computer Science, University of California, San Diego, California 92093
| | - Ravi Sirdeshmukh
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Harsha Gowda
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Charles Wang
- The Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350;
| | - Steven D Leach
- §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
| | - Akhilesh Pandey
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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50
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Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. The sheep genome illuminates biology of the rumen and lipid metabolism. Science 2014; 344:1168-1173. [PMID: 24904168 DOI: 10.1126/science.1252806] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.
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Affiliation(s)
- Yu Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia.,College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Min Xie
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Richard Talbot
- Ediburgh Genomics, University of Edinburgh, Easter Bush, Midlothian EH 25 9RG, UK
| | - Jillian F Maddox
- Department of Veterinary Science, University of Melbourne, Victoria 3010, Australia
| | - Thomas Faraut
- INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France
| | - Chunhua Wu
- Utah State University, Logan, UT 84322-1435-1435, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wenguang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Inner Mongolia Agricultural University, Hohhot 010018, China.,Institute of ATCG, Nei Mongol Bio-Information, Hohhot, China
| | - Jo-Ann Stanton
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Wesley C Barris
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Thibaut Hourlier
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Bronwen L Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - David L Adelson
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Chao Bian
- BGI-Shenzhen, Shenzhen 518083, China
| | - Graham R Cam
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Udaya DeSilva
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Karen Dixen
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | | | - Ian R Franklin
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Shaoyin Fu
- Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Rui Guan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Margaret A Highland
- USDA-ARS Animal Disease Research Unit, Pullman, WA 99164 USA.,Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164 USA
| | - Michael E Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Aaron B Ingham
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Tian Lv
- BGI-Shenzhen, Shenzhen 518083, China
| | - Tittu Mathew
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sean McWilliam
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Moira Menzies
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | | | - David Robelin
- INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France
| | - Bertrand Servin
- INRA, Laboratoire de Génétique Cellulaire, UMR 444, Castanet-Tolosan F-31326, France
| | - David Townley
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | | | - Bin Wei
- BGI-Shenzhen, Shenzhen 518083, China.,Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Stephen N White
- USDA-ARS Animal Disease Research Unit, Pullman, WA 99164 USA.,Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164 USA
| | | | - Chen Ye
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou,730050,China
| | - Peng Zeng
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jacob B Hansen
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Karsten Kristensen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Huw E Jones
- Biosciences KTN, The Roslin Institute, Easter Bush, Midlothian, EH25 9RG, UK
| | - V Hutton Oddy
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - John C McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - James Kijas
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China.,Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Macau University of Science and Technology, Macau 999078, China
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alan L Archibald
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH 25 9RG, UK
| | | | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Brian P Dalrymple
- CSIRO Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
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