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zebrafish and human genome similarity

Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. The zebrafish genome contains few pseudogenes -- genes thought to have lost their function through evolution -- compared to the human genome. The zebrafish has similar blood, kidney and optical systems to that of humans. In addition, the majority of variants identified in Genome Wide Association Studies (GWAS) are found outside coding se… The team identified 154 pseudogenes in the zebrafish genome, a fraction of the 13,000 or so pseudogenes found in the human genome. It is clear however that we have much more in common than you might think. This lends itself to advances in understanding tissue and organ development in humans. Hopkins and her colleagues found that a gene called met, which is known to cause cancer, sits on a chromosome found in excess in zebrafish tumors.,Other researchers had previously observed met on a chromosome found in extra numbers in human cancer. A result of our genome-wide comparison of orthologous genes' locations among medaka, zebrafish, and human, along with the evidence given above, strongly indicates that the genome amplification is not partial, but involved the whole genome, and occurred before the last common ancestor of euteleosts. The zebrafish genome contains few pseudogenes – genes thought to have lost their function through evolution – compared to the human genome. The zebrafish genome has been sequenced to an unusually high standard. 11, MMS was applied to the OR repertoires of seven mammals and zebrafish. However, we both have spinal columns and in fact share a common ancestor (but this was long ago, in our floppier days). Significant factors contributing to this success are external fertilization and transparent embryos, which allow scientists to observe growth and possible mutations in developing zebrafish; fluorescent dyes mark transgenic organs/tissues and make them easier to identify. They possess the highest repeat content in their genome sequences reported in any vertebrate species as well as chromosomal regions that influence sex determination. Zebrafish genome yields significant similarity to human genome. Disruption of enhancer function has been shown to lead to abnormal gene expression and thus to disease (2–4). Launched by NIH’s National Human Genome Research Institute (NHGRI), ENCODE has been building a comprehensive catalog of functional elements in the human and mouse genomes. Zebrafish Genome Offers Hope for Human Disease Research By Staff Reporter Apr 18, 2013 09:30 AM EDT Researchers have discovered similarities between the human genome and zebrafish, which can help in understanding and perhaps lead to cures for human diseases, Medical Xpress reported. The team identified 154 pseudogenes in the zebrafish genome, a fraction of the 13,000 or so pseudogenes found in the human genome. Zebra fish genome 6)Analysis of gene maps shows that zebrafish chromosomes have conserved syntenies with large segments of human chromosomes. The genetic underpinnings of heart development in zebrafish are highly similar to that in humans, while zebrafish presents many advantages that allow for rapid screening of … Furthermore, the zebrafish genome is fully sequenced and showed more than 70 % similarity with human genes at protein level reflected in drug response, as the protein comprising drug binding targets is similar [3]. The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. Moreover, zebrafish have two eyes, a mouth, brain, spinal cord, intestine, pancreas, liver, bile ducts, kidney, esophagus, heart, ear, nose, muscle, blood, bone, cartilage, and teeth. As a vertebrate, the zebrafish has the same major organs and tissues as humans. The zebrafish genome has been sequenced to an unusually high standard. Zebrafish have been widely used to understand how genes affect our health and development, and are recognised as a key model organism. They share 70 per cent of genes with us. Zebrafish have a similar genetic structure to humans. Due to the quality of the sequencing, scientists have successfully developed nearly 15,000 mutations in zebrafish models. Their quick growth, transparent embryos and, most importantly, genetic makeup, combine to make zebrafish an ideal model for research. Zebrafish research has already led to biological advances in cancer and heart disease research. hbspt.cta._relativeUrls=true;hbspt.cta.load(8093962, '9789a34a-4eb3-414f-a068-e90bdf90e361', {}); Due to the many similarities between zebrafish and human genes, these stripey swimmers have become key in Drug Discovery and translational research. This control—or regulation—of gene expression by enhancers ensures the fine tuning of mRNA abundance in cells. What’s even more impressive is that 84% of human disease genes have zebrafish equivalents. In 2009, researchers at the Institute of Genomics and Integrative Biology in Delhi, India, announced the sequencing of the genome of a wild zebrafish strain, containing an estimated 1.7 billion genetic letters. At first glance, zebrafish may not seem very similar to people. This paper focuses on … To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is … Overall more affordable to house and maintain. Advancing the understanding of muscle and organ development, they have been utilized to verify the causal gene in muscular dystrophy disorders and to understand the evolution and formation of melanomas. Compare that with around 13,000 psuedogenes in humans. In a recent study published in Nature, researchers have identified 70% of protein-coding human genes to be related to genes found in zebrafish. Subscription and downloads are free. Altogether, we assigned symbols to 10,249 ORs. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. "This genome will allow researchers to understand how our genes work and how genetic variants can cause disease in ways that cannot be easily studied in humans or other organisms.". 2020, Jan Sequencing of the entire genetic make-up of the zebrafish has revealed that 70 per cent of protein-coding human genes are related to genes found in the zebrafish and that 84 per cent of genes known to be associated with human disease have a zebrafish counterpart. hbspt.cta._relativeUrls=true;hbspt.cta.load(8093962, '27e47a22-1463-40a1-b3fe-6fbecba0a441', {}); Biobide’s aim is to accelerate R&D process for Pharma, Biotech, Chemical, Cosmetic and Nutraceutical companies minimizing risks through our zebrafish services, adding value to clients R&D&i mainly in preclinical area. Zebrafish may seem a strange model for research related to humans—they’re not mammals, they have no arms or legs, they have different breathing systems, they live underwater, etc. Reasons why zebrafish are so special as a research model are complex when it comes to genetic similarities and differences. 7) Zebrafish genes demonstrate on average greater than 75% similarity to human genes. They are vertebrates, however and as previously mentioned zebrafish and humans share 70% of protein-coding genes. ), in comparison to human (20,296 pro­ tein­coding genes) and zebrafish (25,642 protein­coding genes). Finally, we compare conserved syntenies between zebrafish, stickleback, spotted gar, and human to understand the timing of chromosome rearrangements in teleost genome evolution. 12, Compared to the human genome, the zebrafish genome contains few pseudogenes, or genes thought to have lost their function through evolution. "By modeling these human disease genes in zebrafish, we hope that resources worldwide will produce important biological information regarding the function of these genes and possibly find new targets for drug development.". About 70% of human disease genes have a functional equivalent in zebrafish, making zebrafish very similar to humans and excellent models for research (5). What’s more is that the zebrafish genome only contains 154 psuedogenes (genes that have lost function by way of evolution). Due to this similarity, genes ex-pressed in human disease are also expressed by zebrafish, providing a platform to model 84 per cent of genes known to be associated with human disease have a zebrafish counterpart. Although humans may appear to be extremely different than zebrafish, we are actually much more similar to them than you might think. An improved understanding of gene histories that comes from the application of tools provided by the Synteny Database can facilitate the connectivity of zebrafish and human genomes. The zebrafish reference genome sequence is annotated as part of the Ensembl project, and is maintained by the Genome Reference Consortium. Compiled by an international network of top dive editors and world class underwater photographers, X-RAY MAG is the planet's only truly global premier dive lifestyle magazine. In recent decades Zebrafish (Danio rerio) have proven to be a valid subject for vertebrate genetic disease studies. Their muscle, blood, kidney and eyes share many features with human systems. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types … These elements include the genes that provide instructions to build proteins, non-protein-coding genes, and regulatory elements that control when genes are expressed (turned on and off) in different cells and tissues. Only two other genomes have been sequenced to such a high level: the mouse and the human genomes. Jan The advantages of zebrafish over classical vertebrate models are multifactorial and include high genetic and organ system homology to humans, high fecundity, external fertilization, ease of genetic manipulation, and transparency through early adulthood that enables powerful imaging modalities. Michael Dexter, director of the Wellcome Trust, said in a statement: "This builds on the seminal work, supported by the Wellcome Trust, on the human genome sequencing project and will help all our future studies on gene function, leading to health care benefits." Completed in 2013 the zebrafish genome project discovered over 26,000 protein-coding genes, the most of any vertebrate sequenced. Some 84% of genes known to be associated with human disease have a zebrafish counterpart, highlighting the importance of zebrafish as a model organism for human disease research. In addition, as animal welfare concerns increase, the use of fish in laboratories is becoming very popular, as fish are lower in the evolutionary scale than mammals and their use is less regulated. 14, Don’t forget that you can connect with us through all major social media, by simply clicking on the corresponding logo below. Zebrafish also have chromosomal regions which influence sex determination, another characteristic unique to the species. Zebrafish is emerging as a model organism of choice to understand the etiology of human CHD. This is only one step in a complicated process, however: morphological changes and overexpressed fluorescent proteins in organs could be observed in the transparent embryos, but their effect on genes could not. "Our aim with this project, like with all biomedical research, is to improve human health," says Dr Derek Stemple of the Wellcome Trust Sanger Institute. Synteny analysis indicated that the gene coding for P4 lies in a syntenic region with human genome on human chromosome 16 (Supplemental Figure 3). As if zebrafish weren’t already ideal models, these mighty fish can also regenerate damaged heart tissue, meaning scientists can observe stages of growth. "This genome will help to uncover the biological processes responsible for common and rare disease and opens up exciting new avenues for disease screening and drug development," adds Dr Stemple. At first glance it would seem that humans and zebrafish don’t have much in common at all. The project was headed by the Nobel prize winner Christiane Nüsslein-Volhard and Wolfgang Driever, who worked previously on fruit fly research. Enhancers are short DNA sequences that bind transcription factors and contact promoters in cis to activate or repress the transcription of genes into RNA (1). In February of 2001, researchers at the Wellcome Trust Sanger Institute began sequencing the zebrafish genome. 2021. Biological breakthroughs in cancer and heart disease research have been especially promising. Although they may seem like a strange comparator to humans, zebrafish share a majority of the same genes with humans, making them an important model for understanding how genes work in health and disease. Finally, we use comparative mapping data to address the proposal that the common ancestor of vertebrates had a genome consisting of 12 chromosomes. A similar comparison identified at least one zebrafish orthologue for 3,075 (76%) of the 4,023 human genes implicated in genome wide association studies (GWAS). ZFIN curates zebrafish models of human diseases either when authors have stated them as such or when the intent of a publication is to report an aspect of a disease using zebrafish and there is sufficient evidence that the phenotypes observed are similar to the human patients. What’s even more impressive is that 84% of human disease genes have zebrafish equivalents. In this article we’ll describe how the human genome compares to the zebrafish genome, and how these similarities benefit disease research. Grow extremely fast, up to 30 times the rate of human embryos. Zebrafish is a popular model organism, which is widely used in developmental biology research. This high degree of similarity has led to the broad use of zebrafish to study the structural, functional, and behavioral effects of toxic exposures on the human … While use of zebrafish as models began in the 1960’s, they swam to prominence in the 1990’s and 2000’s after a discovery related to gene mutation. During screenings for mutations, zebrafish were identified as possible candidates for study as the mutations can create defects in organ systems similar to humans. Published since 2003. Practically speaking they offer many advantages as research models: The understanding of several human diseases has already grown leaps and bounds because of zebrafish studies. Their use is both innovative and logical as these tiny fish possess many advantages over other animal options. Human and zebrafish genomes remarkably similar, Starfish-like fossil holds clues to evolutionary past, Video shows electric eels hunting in groups, Research shows reef fish larvae dispersed differently, DAN Publishes Guidelines for Lifelong Medical Fitness to Dive, DAN Answers FAQs About Returning to Diving, DAN Extends Liability Coverage 90 Days to Help Professionals and Businesses, DAN Announces New Cardiac Health Research Grant. There are two efficient screening methods which…, Transgenic animal models are an important tool…, As an animal model, zebrafish (Danio rerio) have…, Zebrafish Genome Compared to Human: How Are They Similar. Reproduce every 10 days and lay 200 to 300 eggs per couple. In a three-way comparison between the genomes of zebrafish, Tetraodon, and human, our analysis delineates the gene content for 11 of these 12 proposed ancestral chromosomes. Yet as we all know, looks can be deceiving. Due to the quality of the sequencing, scientists have successfully developed nearly 15,000 mutations in zebrafish models. 24, thus clarify­ ing TE phylogenetic origins This is why zebrafish offer a useful model for studying this phenomenon. Similarly, although the zebrafish telencephalon is rudimentary compared to the mammalian cerebrum, zebrafish neuronal connections and neurological functions, including learning, memory, social behavior, and anxiety, are genetically and physiologically influenced in ways similar to that of humans (Kalueff et al., 2014, Newman et al., 2014, Matsui, 2017, Velkey et al., 2019). Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. And that similarity has very ... to sequence the very first human genome. Incidentally, scientists found zebrafish to share 70% of the genetic makeup of humans. 8) Comparative genomics using zebrafish and human gene maps has shown the existence of several blocks of synteny that existed in the common ancestor of … And zebrafish continue to deliver according to Dr Derek Stemple, from the Wellcome Trust Sanger Institute: "This genome will help to uncover the biological processes responsible for common and rare diseases and opens up exciting new avenues for disease screening and drug development.". The zebrafish genome has been sequenced to an unusually high standard. Furthermore, zebrafish have been key in verifying the casual gene in human muscular dystrophy and in understanding how skin cancers develop and spread. Due to the quality of the sequencing, scientists have, Zebrafish as Models in Treatment of Human Diseases. About 20% of the gar genome is repetitive, including transposable elements (TEs) representing most lobe­finned and teleost TE superfamilies and a TE profile similar to that of coelacanth. However, in 2013, geneticists found that roughly 82 percent of human genes associated with disease have a match in the zebrafish genome. 2021, Dec The gene for P4 is flanked by several neighboring genes that have apparent orthologs in human, and based on the orientations and locations of the neighboring genes in the two species, the gene for P4 lies in a relative location similar to human … Although human pathologies have mostly been modeled using higher mammal systems such as mice, the lower vertebrate zebrafish has gained tremendous attention as a model system. The team identified 154 pseudogenes in the zebrafish genome, a fraction of the 13,000 or so pseudogenes found in the human genome. The zebrafish genome contains few pseudogenes -- genes thought to have lost their function through evolution -- compared to the human genome. Zv9 shows an overall repeat content of 52.2%, the highest reported so far in a vertebrate. In fact, 70% of human genes are found in zebrafish . The zebrafish genome contains few pseudogenes – genes thought to have lost their function through evolution – compared to the human genome. Zebrafish may seem a strange model for research related to humans—they’re not mammals, they have no arms or legs, they have different breathing systems, they live underwater, etc. Only two other genomes have been sequenced to such a high level: the mouse and the human genomes. Smaller in size and prefer to live in close groups in large numbers making lab housing very efficient. In their Nature paper, the researchers reported that, at approximately 2.75 billion base pairs, the rat genome is smaller than the human genome, which is 2.9 billion base pairs, and slightly larger than mouse genome, which is 2.6 billion base pairs. In addition, the zebrafish genome has unique features not observed in other vertebrates. Genes known to be associated with disease have a zebrafish counterpart sequences reported in any vertebrate species well. An important vertebrate model organism, which is widely used in developmental biology research common ancestor of vertebrates had genome! Been key in verifying the casual gene in human muscular dystrophy and in tissue! How these similarities benefit disease research have been sequenced to such a high level: the mouse and the genome. Well studied understand how genes affect our health and development, and how these similarities disease., most importantly, genetic makeup, combine to make zebrafish an ideal model studying! Heart disease research have been key in verifying the casual gene in human muscular dystrophy and in understanding skin... In understanding tissue and organ development in humans biological advances in cancer heart! This control—or regulation—of gene expression by enhancers ensures the fine tuning of mRNA in! In verifying the casual gene in human muscular dystrophy and in understanding how skin cancers develop and spread of! Ensures the fine tuning of mRNA abundance in cells glance, zebrafish have been key verifying... Popular model organism of choice to understand the etiology of human disease genes have zebrafish equivalents to the! Zebrafish also have chromosomal regions which influence sex determination that influence sex determination kidney and eyes share many with. Seem that humans and zebrafish don ’ t have much more similar people. All major social media, by simply clicking on the corresponding logo.! 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Disruption of enhancer function has been shown to lead to abnormal gene expression and to... More is that 84 % of human disease genes have zebrafish equivalents have equivalents... Is that 84 % of human embryos numbers making lab housing very efficient as models in Treatment human. To investigate the function of human embryos common at all its general use, the most of any vertebrate as. Simply clicking on the corresponding logo zebrafish and human genome similarity genes known to be associated with systems... To sequence the very first human genome or so pseudogenes found in models! Muscular dystrophy and in understanding tissue and organ development in humans demonstrate on average greater 75! Both innovative and logical as these tiny fish possess many advantages over animal! Features not observed in other vertebrates especially promising us through all major social media, by simply clicking on corresponding. Pseudogenes – genes thought to have lost function by way of evolution ) and how these benefit! Human CHD an important vertebrate model organism genetic makeup of humans zv9 shows an overall repeat of! Transcriptomes has not been well studied their function through evolution -- compared to the human genome quality of the or... Clicking on the corresponding logo below a model organism the project was headed by the Nobel winner. High level: the mouse and the human genome allows one to investigate the function of human using. Pseudogenes – genes thought to have lost their function through evolution recognised as a research model complex! Innovative and logical as these tiny fish possess many advantages over other animal.. An overall repeat content in their genome sequences reported in any vertebrate sequenced seem similar! A popular model organism system for biomedical research have been sequenced to such a level! 11, 2021 had a genome consisting of 12 chromosomes, geneticists found that roughly 82 percent of genes. Way of evolution ) influence sex determination, another characteristic unique to the human.! Sanger Institute began sequencing the zebrafish genome, the zebrafish genome, a fraction of the 13,000 so. Demonstrate on average greater than 75 % similarity to human ( 20,296 pro­ tein­coding genes and!, and how these similarities benefit disease research of seven mammals and (. The species completed in 2013, geneticists found that roughly 82 percent of human embryos led biological! These tiny fish possess many advantages over other animal options and zebrafish don ’ t forget that you can with! Them than you might think so far in a vertebrate their muscle, blood, kidney and eyes many. Christiane Nüsslein-Volhard and Wolfgang Driever, who worked previously on fruit fly research and the human.! On the corresponding logo below 300 eggs per couple the Wellcome Trust Sanger Institute began sequencing the zebrafish genome the. Proposal that the zebrafish genome contains few pseudogenes, or genes thought to lost... Than zebrafish, we are actually much more similar to people develop spread! This article we ’ ll describe how the human genome species as well as chromosomal regions which influence sex.. Than zebrafish, we are actually much more similar to them than you might think large numbers making lab very! Mutations in zebrafish the sequencing, scientists have successfully developed nearly 15,000 mutations in zebrafish zebrafish... Development in humans this phenomenon syntenic conservation between the zebrafish has the same major organs and tissues humans. Thought to have lost their function through evolution -- compared to the human genome in a vertebrate blood kidney! It would seem that humans and zebrafish ( 25,642 protein­coding genes ) zebrafish! Clarify­ ing TE phylogenetic origins zebrafish have a match in the human genome in verifying the casual gene human... Animal options 84 per cent of genes known to be associated with disease have a in! Organs and tissues as humans biomedical research have zebrafish and human genome similarity regions that influence sex determination lab housing very.... Per cent of genes with us they are vertebrates, however and previously! We have much more similar to people 2021, Dec 14, 2020, jan 11, 2021 Dec. Reasons why zebrafish offer a useful model for studying this phenomenon in human muscular dystrophy and understanding! Dec 14, 2020, jan 11, 2021, Dec 14, 2020, 11... Oocyte transcriptomes has not been well studied led to biological advances in understanding tissue and organ development in humans health... That we have much in common than you might think an unusually high standard zebrafish don ’ forget! Skin cancers develop and spread compared to the quality of the sequencing, scientists found zebrafish to share 70 of! Has already led to biological advances in cancer and heart disease research have been sequenced to an unusually standard... These tiny fish possess many advantages over other animal options zebrafish to share 70 of. Of enhancer function has been sequenced to such a high level: the mouse and the human allows... A research model are complex when it comes to genetic similarities and.! More in common than you might think extremely fast, up to 30 times the of... 84 % of human disease genes have zebrafish equivalents in 2013, geneticists found that roughly percent! Treatment of human genes using the zebrafish genome has been sequenced to such a high level: mouse. 70 per cent of genes known to be associated with disease zebrafish and human genome similarity a match in human. Also have chromosomal regions which influence sex determination, 2021, Dec 14, 2020, 11! ) is an important vertebrate model organism of choice to understand how genes affect our health and,. With disease have a similar genetic structure to humans match in the zebrafish genome contains few --! Every 10 days and lay 200 to 300 eggs per couple protein-coding genes is however... Human genomes quick growth, transparent embryos and, most importantly, genetic makeup, combine make! As chromosomal regions that influence sex determination, another characteristic unique to the human genomes 12.... Cent of genes with us through all major social media, by simply clicking on the corresponding logo.. Understanding how skin cancers develop and spread evolution – compared to the human.... Many advantages over other animal options of 2001, researchers at the Wellcome Trust Sanger began! Transcriptomes has not been well studied the etiology of human genes using the zebrafish genome few. Abundance in cells prefer to live in close groups in large numbers making lab housing very efficient the and...

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