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Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.
Functional genomics is a field of molecular biology that attempts to describe gene functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects. Functional genomics focuses on the dynamic aspects such as gene transcription, translation, regulation of gene expression and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional "candidate-gene" approach.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
The Consortium for the Barcode of Life (CBOL) was an international initiative dedicated to supporting the development of DNA barcoding as a global standard for species identification. CBOL's Secretariat Office is hosted by the National Museum of Natural History, Smithsonian Institution, in Washington, DC. Barcoding was proposed in 2003 by Prof. Paul Hebert of the University of Guelph in Ontario as a way of distinguishing and identifying species with a short standardized gene sequence. Hebert proposed the 658 bases of the Folmer region of the mitochondrial gene cytochrome-C oxidase-1 as the standard barcode region. Hebert is the Director of the Biodiversity Institute of Ontario, the Canadian Centre for DNA Barcoding, and the International Barcode of Life Project (iBOL), all headquartered at the University of Guelph. The Barcode of Life Data Systems (BOLD) is also located at the University of Guelph.
Conogethes is a genus of moths in the subfamily Spilomelinae of the family Crambidae. The currently 17 recognized species are distributed in the Indomalayan and Australasian realm.
Sisyracera is a genus of snout moths in the subfamily Spilomelinae of the family Crambidae. It was described in 1890 by Heinrich Benno Möschler with Leucinodes preciosalis as type species, now considered a synonym of Sisyracera subulalis. The genus has been placed in the tribe Udeini.
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections, an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These "barcodes" are sometimes used in an effort to identify unknown species or parts of an organism, simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries.
The history of genetics can be represented on a timeline of events from the earliest work in the 1850s, to the DNA era starting in the 1940s, and the genomics era beginning in the 1970s.
Eupithecia abdera is a moth in the family Geometridae. It is known from Ecuador, where the holotype, an adult male specimen, was collected at an altitude of 3400 m.
Nosferatu is a genus of cichlid fishes endemic to the Rio Panuco Basin and the tributaries of the adjacent Tamiahua Lagoon and San Andrés Lagoon in the states of Veracruz, Hidalgo, San Luis Potosí, Tamaulipas and Querétaro, Mexico. The genus is characterized by a prolongation in the size of the symphysial pair of teeth relative to that of the other teeth in the outer row of the upper jaw ; breeding pigmentation that consists of darkening of ventral area extending over nostrils, opercular series, and pectoral fins; depressed dorsal fin rarely expands beyond anterior third of caudal fin; and an elongated, elastic, smooth caecum adhered to a saccular stomach.
Pollen DNA barcoding is the process of identifying pollen donor plant species through the amplification and sequencing of specific, conserved regions of plant DNA. Being able to accurately identify pollen has a wide range of applications though it has been difficult in the past due to the limitations of microscopic identification of pollen.
DNA barcoding is an alternative method to the traditional morphological taxonomic classification, and has frequently been used to identify species of aquatic macroinvertebrates. Many are crucial indicator organisms in the bioassessment of freshwater and marine ecosystems.
Microbial DNA barcoding is the use of DNA metabarcoding to characterize a mixture of microorganisms. DNA metabarcoding is a method of DNA barcoding that uses universal genetic markers to identify DNA of a mixture of organisms.
DNA barcoding methods for fish are used to identify groups of fish based on DNA sequences within selected regions of a genome. These methods can be used to study fish, as genetic material, in the form of environmental DNA (eDNA) or cells, is freely diffused in the water. This allows researchers to identify which species are present in a body of water by collecting a water sample, extracting DNA from the sample and isolating DNA sequences that are specific for the species of interest. Barcoding methods can also be used for biomonitoring and food safety validation, animal diet assessment, assessment of food webs and species distribution, and for detection of invasive species.
DNA barcoding in diet assessment is the use of DNA barcoding to analyse the diet of organisms. and further detect and describe their trophic interactions. This approach is based on the identification of consumed species by characterization of DNA present in dietary samples, e.g. individual food remains, regurgitates, gut and fecal samples, homogenized body of the host organism, target of the diet study.
Winifred Hallwachs is an American tropical ecologist who helped to establish and expand northwestern Costa Rica's Área de Conservación Guanacaste (ACG). The work of Hallwachs and her husband Daniel Janzen at ACG is considered an exemplar of inclusive conservation.
Fungal DNA barcoding is the process of identifying species of the biological kingdom Fungi through the amplification and sequencing of specific DNA sequences and their comparison with sequences deposited in a DNA barcode database such as the ISHAM reference database, or the Barcode of Life Data System (BOLD). In this attempt, DNA barcoding relies on universal genes that are ideally present in all fungi with the same degree of sequence variation. The interspecific variation, i.e., the variation between species, in the chosen DNA barcode gene should exceed the intraspecific (within-species) variation.
Genome skimming is a sequencing approach that uses low-pass, shallow sequencing of a genome, to generate fragments of DNA, known as genome skims. These genome skims contain information about the high-copy fraction of the genome. The high-copy fraction of the genome consists of the ribosomal DNA, plastid genome (plastome), mitochondrial genome (mitogenome), and nuclear repeats such as microsatellites and transposable elements. It employs high-throughput, next generation sequencing technology to generate these skims. Although these skims are merely 'the tip of the genomic iceberg', phylogenomic analysis of them can still provide insights on evolutionary history and biodiversity at a lower cost and larger scale than traditional methods. Due to the small amount of DNA required for genome skimming, its methodology can be applied in other fields other than genomics. Tasks like this include determining the traceability of products in the food industry, enforcing international regulations regarding biodiversity and biological resources, and forensics.
Metabarcoding is the barcoding of DNA/RNA in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does not focus on one specific organism, but instead aims to determine species composition within a sample.
References
- ↑ Ratnasingham, Sujeevan; Hebert, Paul D. N. (2013). "A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System". PLOS ONE. 8 (7): e66213. Bibcode:2013PLoSO...866213R. doi: 10.1371/journal.pone.0066213 . ISSN 1932-6203. PMC 3704603 . PMID 23861743.
- 1 2 RATNASINGHAM, SUJEEVAN; HEBERT, PAUL D. N. (2007-01-24). "BARCODING: bold: The Barcode of Life Data System (http://www.barcodinglife.org)". Molecular Ecology Notes. 7 (3): 355–364. doi: 10.1111/j.1471-8286.2007.01678.x . ISSN 1471-8278. PMC 1890991 . PMID 18784790.
- 1 2 "BOLD Print Handbook for BOLD v4". www.boldsystems.org. Retrieved 2020-11-16.
- ↑ "Kingdoms of Life Being Barcoded | BOLDSYSTEMS". www.boldsystems.org. Retrieved 2020-11-16.
- ↑ "BARCODE 500K". ibol.org.
