Genomics categories & taxonomy
agricultural genomics: Agricultural biotechnology continues to benefit from the insights being developed during the era of the Human Genome Project. The proliferation of mapping, genotyping, and diagnostic methodologies has rapidly expanded the analytical tools available to crop scientists for the analysis and utilization of plant genomes. Related terms: crop genomics, environmental genomics, food genomics, nutritional genomics, plant genomics; Model & other organisms glossary Arabidopsis
Agricultural genomics links:
combinatorial genomics: Similar in concept to required for recognition of all items in long- term memory combinatorial chemistry, this technology shuffles portions of genes to give a vast number of new combinations, which are then screened for a desired function. Enhanced function, or even new functions, can be generated by repeating the cycle circuits many times to "evolve" optimized recombinants in vitro. [Department of Defense Critical Technologies Part III: Developing Critical Technologies Section 3: Biological Technology, July 1999] Related terms: Combinatorial libraries & synthesis glossary combinatorial chemistry;
crop genomics: Molecular technologies, techniques and breeding strategies associated with plants of agricultural importance. Related terms: agricultural genomics, plant genomics, nutritional genomics
environmental genomics: This programme will apply genomics to the natural environment, using sequence data to advance and test evolutionary and ecological theory, and so provide a better understanding of ecosystem function in the context of biodiversity (intraspecific genetic variation, species richness and perceived redundancy). Related terms: ecological genomics, plant genomics; Pharmacogenomics glossary toxicogenomics
forward genetics: the approach of determining the genetic basis responsible for a phenotype. This was initially done by using naturally occurring mutations or inducing mutants with radiation, chemicals, or insertional mutagenesis (e.g. transposable elements). Subsequent breeding takes place, mutant individuals are isolated, and then the gene is mapped. Forward genetics can be thought of as a counter to reverse genetics, which determines the function of a gene by analyzing the phenotypic effects of altered DNA sequences. Wikipedia accessed 2018 Nov https://en.wikipedia.org/wiki/Forward_genetics
The traditional approach to genetics, which starts with a phenotype and then identifies genetic mutations or variations that control or cause that trait. Related term: positional cloning. Compare reverse genetics
forward genomics: Given the advances in next-generation sequencing, a veritable zoo of genomic data from hundreds of animals have now been sequenced, allowing scientists unprecedented insights into how DNA changes may underlie the differences between species and the diversity of life on Earth. When viewed through the prism of evolution, these DNA changes either discard ancestral traits or gain entirely new ones, for example, in key senses like vision, speech and hearing. Now, in a new study, Prudent et al. (2016) have developed new computational approaches, called “Forward Genomics” which can hone in on key genomic locations amongst the millions of DNA changes that occurred between different species. Joseph Caspermeyer; New “Forward Genomics” Approach to Identify Keys to Loss of Vision in Blind Mammals, Molecular Biology and Evolution, Volume 33, Issue 8, 1 August 2016, Pages 2175, https://doi.org/10.1093/molbev/msw136 https://academic.oup.com/mbe/article/33/8/2175/2579436 Narrower terms: Post-Transcriptional Gene Silencing PTGS, RNA silencing; Related term: epigenetics
genomics: The systematic study of the complete DNA sequences (GENOME) of organisms. [MeSH, 2001] More under genomics: Genomics glossary Basic genetics & genomics (tries to) answer the question of what the difference between genetics and genomics is.
genome transplantation: As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Carole Lartigue 1, John I. Glass 1*, Nina Alperovich 1, Rembert Pieper 1, Prashanth P. Parmar 1, Clyde A. Hutchison III 1, Hamilton O. Smith 1, J. Craig Venter , Genome Transplantation in Bacteria: Changing One Species to Another, Science Published Online June 28, 2007, Science DOI: 10.1126/science.1144622
genomic library: Gene categories
high-throughput genomics: Genomic studies are now approaching "industrial" speed and scale, thanks to advances in gene sequencing and the increasing availability of high- throughput methods for studying genes, the proteins they encode, and the pathways in which they are involved. Data can now be acquired on many genes at once, either sequentially or in parallel. It is also possible to expand the range of genomic effects being examined. The abundance of new data available means that more targets should now be identifiable, but the key to finding such new targets will be to use the right combination of technologies and have them ideally integrated. Related terms: Bioinformatics high throughput Drug discovery & development target validation.
industrial genomics: Genomics scaled up to industrial strength and throughput. Related term: high throughput genomics
integrative genomics: According to PubMed, published research studies involving integrated analysis of multiple ‘omic data types have witnessed a nearly 10-fold increase over the past decade. The reasons for the surge in integrative genomics studies are both biological – fueled by an increasing understanding that the development and progression of complex diseases are due to the confluence of alterations in the genome, epigenome, transcriptome, proteome, etc. (and their complex interactions) – and logistical – while large-scale integrative ‘omic studies were once economically infeasible, the declining cost of high-throughput technologies for interrogating the ‘ome have opened the door for such studies to become a reality. Koestler DC, Jones MJ, Kobor MS. The era of integrative genomics: more data or better methods? Epigenomics. 2014;6(5):463-7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414242/
intergenomics: The bioinformatics competence center "Intergenomics" in Braunschweig has the scientific goal to develop bioinformatic tools for modeling of the interactivity of genome- driven bacterial infection processes in mammals and plants. Bioinformatics research and education in Germany. Dietmar Schomburg, Martin Vingron, In Silico Biology 2, 0015, 2002 http://www.bioinfo.de/isb/2002/02/0015/main.html
metagenome: Historically, biotechnology has missed up to 99% of existing microbial resources by using traditional screening techniques. Strategies of directly cloning 'environmental DNA' comprising the genetic blueprints of entire microbial consortia (the so-called 'metagenome') provide molecular sequence space that along with ingenious in vitro evolution technologies will act synergistically to bring a maximum of available sequence- space into biocatalytic application. Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Lorenz P, Liebeton K, Niehaus F, Eck J. Curr Opin Biotechnol 2002 Dec;13(6): 572- 577 Related terms: microbiome
metagenomics: is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. … The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F. Brady, and others, and first appeared in publication in 1998.The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome. Recently, Kevin Chen and Lior Pachter (researchers at the University of California, Berkeley) defined metagenomics as "the application of modern genomics technique without the need for isolation and lab cultivation of individual species". Wikipedia http://en.wikipedia.org/wiki/Metagenomics accessed Oct 19 2017
The committee will convene a workshop and other appropriate information gathering activities in order to define the scope of metagenomics, understand how it is being used now in various disciplines, the technical approaches being used by different groups, and how metagenomics may develop in the future. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet, Board on Life Sciences , National Academies Press, 2007 http://books.nap.edu/openbook.php?record_id=11902&page=151
The genetic complement of a
microorganism as represented in its DNA or in some microorganisms its RNA. MeSH
Year introduced: 2014
sequencing of mammoth DNA. "We sequenced 28 million base pairs of DNA in a
metagenomics approach using a woolly mammoth (Mammuthus
primigenius) sample from Siberia … The high percentage of
endogenous DNA recoverable from this single mammoth would allow for
completion of its genome, unleashing the field of paleogenomics."
to Paleogenomics: Large-Scale Sequencing of Mammoth DNA, Hendrik N.
Poinar 1*, Carsten Schwarz 2, Ji Qi 3, Beth
Shapiro 4, Ross D. E. MacPhee 5, Bernard Buigues 6,
Alexei Tikhonov 7, Daniel Huson 8, Lynn P. Tomsho 3,
Alexander Auch 3, Markus Rampp 9, Webb Miller 3,
Stephan C. Schuster 3*
subtractive genomics: One of the recently adopted strategies is based on a subtractive genomics approach, in which the subtraction dataset between the host and pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used successfully in recent times to identify essential genes in Pseudomonas aeruginosa. Anirban Dutta1, Shashi Kr. Singh1, Payel Ghosh1, Runni Mukherjee1, Sayak Mitter1 and Debashis Bandyopadhyay2, In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori, In Silico Biology 6, 0005 (2006); ©2006, Bioinformation Systems e.V. http://www.bioinfo.de/isb/2006/06/0005/main.html
IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.
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