The Functional Genomics of Model Organisms: Addressing Old Questions from a New Perspective

2005 ◽  
pp. 325-375
Author(s):  
Dorothea K. Thompson ◽  
Jizhong Zhou
Keyword(s):  
Functional Genomics ◽  
Model Organisms ◽  
New Perspective

scholarly journals Functional genomics and proteomics of the cellular osmotic stress response in `non-model' organisms

2007 ◽  
Vol 210 (9) ◽  
pp. 1593-1601 ◽  
Author(s):  
D. Kultz ◽  
D. Fiol ◽  
N. Valkova ◽  
S. Gomez-Jimenez ◽  
S. Y. Chan ◽  
...  
Keyword(s):  
Stress Response ◽  
Osmotic Stress ◽  
Functional Genomics ◽  
Model Organisms ◽  
Genomics And Proteomics ◽  
Osmotic Stress Response

scholarly journals Genome sequence of the model rice variety KitaakeX

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rashmi Jain ◽  
Jerry Jenkins ◽  
Shengqiang Shu ◽  
Mawsheng Chern ◽  
Joel A. Martin ◽  
...  
Keyword(s):  
Functional Genomics ◽  
De Novo ◽  
Rice Variety ◽  
Rice Genome ◽  
Life Cycles ◽  
Model Organisms ◽  
High Quality ◽  
Rice Varieties ◽  
Protein Coding ◽  
High Quality Genome

Abstract Background The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. Conclusions The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.

Of Mice and Worms: Novel Insights Into ClC-2 Anion Channel Physiology

Physiology ◽  
2002 ◽  
Vol 17 (1) ◽  
pp. 11-16 ◽  
Author(s):  
Kevin Strange
Keyword(s):  
Functional Genomics ◽  
Anion Channel ◽  
Model Organisms ◽  
Anion Channels ◽  
Evolutionary Time

ClC anion channels are found in all major groups of organisms. Recent studies in nematodes and mice suggest that the function and regulation of ClC-2 have been conserved over vast evolutionary time spans. These studies illustrate the experimental advantages of using genomically defined nonmammalian model organisms for characterizing ClC channel functional genomics.

scholarly journals Bioadhesion in ascidians: a developmental and functional genomics perspective

2015 ◽  
Vol 5 (1) ◽  
pp. 20140061 ◽  
Author(s):  
Roberta Pennati ◽  
Ute Rothbächer
Keyword(s):  
Functional Genomics ◽  
Marine Invertebrates ◽  
Marine Species ◽  
Sister Group ◽  
Model Organisms ◽  
Phylogenetic Position ◽  
Adhesive Properties ◽  
Marine Animals ◽  
Fouling Organism ◽  
Adhesive Organs

The development of bioadhesives inspired from marine animals is a promising approach to generate new tissue-compatible medical components. A number of marine species, through their adhesive properties, also represent significant foulers that become increasingly problematic to aquaculture, shipping or local biodiversity. In order to develop more sophisticated man-made glues and/or efficient fouling resistant surfaces, it is important to understand the mechanical, structural and molecular properties of adhesive organs in selected species. Ascidians are marine invertebrates with larvae that opportunistically attach to almost any type of submerged surface to undergo metamorphosis into permanently sessile adults. Not only do they represent a globally important fouling organism, but they are becoming increasingly popular as model organisms for developmental biology. The latter is due to their phylogenetic position as the sister group to the vertebrates and their cellular and molecular accessibility for experimentation. In this paper, we review the mechanisms of larval adhesion in ascidians and draw conclusions from comparative analyses of selected species. We further discuss how knowledge from a developmental and functional genomics point of view can advance our understanding of cellular and molecular signatures and their hierarchical usage in animal adhesive organs.

scholarly journals Functional genomics in the wild: a case study with paper wasps shows challenges and prospects for RNA interference in ecological systems

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 266-272 ◽  
Author(s):  
S.A. Weiner ◽  
A.G. Geffre ◽  
A.L. Toth
Keyword(s):  
Rna Interference ◽  
Functional Genomics ◽  
Gene Function ◽  
Ecological Model ◽  
Model Organisms ◽  
Natural Environments ◽  
Paper Wasps ◽  
Fatty Acid Binding ◽  
In The Wild

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes (NADH dehydrogenase (NADHdh) and retinoid and fatty acid binding protein (RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field.

Integrative Physiology and Functional Genomics of Epithelial Function in a Genetic Model Organism

2003 ◽  
Vol 83 (3) ◽  
pp. 687-729 ◽  
Author(s):  
JULIAN A. T. DOW ◽  
SHIREEN A. DAVIES
Keyword(s):  
Functional Genomics ◽  
Genetic Model ◽  
Model Organism ◽  
Model Organisms ◽  
Integrative Physiology ◽  
Molecular Approaches ◽  
Physiological Analysis ◽  
Organ Level ◽  
And Control ◽  
Reductionist Approach

Dow, Julian A. T, and Shireen A. Davies. Integrative Physiology and Functional Genomics of Epithelial Function in a Genetic Model Organism. Physiol Rev 83: 687–729, 2003; 10.1152/physrev.00035.2002.—Classically, biologists try to understand their complex systems by simplifying them to a level where the problem is tractable, typically moving from whole animal and organ-level biology to the immensely powerful “cellular” and “molecular” approaches. However, the limitations of this reductionist approach are becoming apparent, leading to calls for a new, “integrative” physiology. Rather than use the term as a rallying cry for classical organismal physiology, we have defined it as the study of how gene products integrate into the function of whole tissues and intact organisms. From this viewpoint, the convergence between integrative physiology and functional genomics becomes clear; both seek to understand gene function in an organismal context, and both draw heavily on transgenics and genetics in genetic models to achieve their goal. This convergence between historically divergent fields provides powerful leverage to those physiologists who can phrase their research questions in a particular way. In particular, the use of appropriate genetic model organisms provides a wealth of technologies (of which microarrays and knock-outs are but two) that allow a new precision in physiological analysis. We illustrate this approach with an epithelial model system, the Malpighian (renal) tubule of Drosophila melanogaster. With the use of the beautiful genetic tools and extensive genomic resources characteristic of this genetic model, it has been possible to gain unique insights into the structure, function, and control of epithelia.

scholarly journals Genome sequence of the model rice variety KitaakeX

2019 ◽  
Author(s):  
Rashmi Jain ◽  
Jerry Jenkins ◽  
Shengqiang Shu ◽  
Mawsheng Chern ◽  
Joel A. Martin ◽  
...  
Keyword(s):  
Functional Genomics ◽  
De Novo ◽  
Rice Variety ◽  
Rice Genome ◽  
Life Cycles ◽  
Model Organisms ◽  
High Quality ◽  
Japonica Variety ◽  
Rice Varieties ◽  
Protein Coding

Abstract Background: The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results: Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. Conclusions: The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.

scholarly journals Mice and humans: chromosome engineering and its application to functional genomics.

2002 ◽  
Vol 49 (3) ◽  
pp. 553-569 ◽  
Author(s):  
Jan Klysik
Keyword(s):  
Functional Genomics ◽  
Gene Targeting ◽  
Scaling Up ◽  
Model Organisms ◽  
Functional Modeling ◽  
Cellular Functions ◽  
Chromosome Engineering ◽  
Genetic Traits ◽  
Human Genes ◽  
Mammalian Genes

Functional modeling of human genes and diseases requires suitable mammalian model organisms. For its genetic malleability, the mouse is likely to continue to play a major role in defining basic genetic traits and complex pathological disorders. Recently, gene targeting techniques have been extended towards developing new engineering strategies for generating extensive lesions and rearrangements in mouse chromosomes. While these advances create new opportunities to address similar aberrations observed in human diseases, they also open new ways of scaling-up mutagenesis projects that try to catalogue and annotate cellular functions of mammalian genes.

scholarly journals Functional genomics: lessons from yeast

2002 ◽  
Vol 357 (1417) ◽  
pp. 17-23 ◽  
Author(s):  
Stephen G. Oliver
Keyword(s):  
Functional Analysis ◽  
Functional Genomics ◽  
Complete Genome ◽  
Systematic Approach ◽  
Single Gene ◽  
Model Organisms ◽  
Human Pathogens ◽  
Genome Sequences ◽  
Integrative View ◽  
Yeast Genes

Functional genomics represents a systematic approach to elucidating the function of the novel genes revealed by complete genome sequences. Such an approach should adopt a hierarchical strategy since this will both limit the number of experiments to be performed and permit a closer and closer approximation to the function of any individual gene to be achieved. Moreover, hierarchical analyses have, in their early stages, tremendous integrative power and functional genomics aims at a comprehensive and integrative view of the workings of living cells. The first draft of the human genome sequence has just been produced, and the complete genome sequences of a number of eukaryotic human pathogens (including the parasitic protozoa Plasmodium, Leishmania, and Trypanosoma ) will soon be available. However, the most rapid progress in the elucidation of gene function will initially be made using model organisms. Yeast is an excellent eukaryotic model and at least 40% of single–gene determinants of human heritable diseases find homologues in yeast. We have adopted a systematic approach to the functional analysis of the Saccharomyces cerevisiae genome. A number of the approaches for the functional analysis of novel yeast genes are discussed. The different approaches are grouped into four domains: genome, transcriptome, proteome, and metabolome. The utility of genetic, biochemical, and physico–chemical methods for the analysis of these domains is discussed, and the importance of framing precise biological questions, when using these comprehensive analytical methods, is emphasized. Finally, the prospects for elucidating the function of protozoan genes by using the methods pioneered with yeast, and even exploiting Saccharomyces itself, as a surrogate, are explored.

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