Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; these enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, respond to their environments.. Metabolic reactions may be categorized as catabolic - the breaking down of compounds. Catabolism releases energy, anabolism consumes energy; the chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts - they allow a reaction to proceed more - and they allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals; the basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions. A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants; these similarities in metabolic pathways are due to their early appearance in evolutionary history, their retention because of their efficacy. Most of the structures that make up animals and microbes are made from three basic classes of molecule: amino acids and lipids; as these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion.
These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymes. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. Proteins are important in cell signaling, immune responses, cell adhesion, active transport across membranes, the cell cycle. Amino acids contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress. Lipids are the most diverse group of biochemicals, their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform.
The fats are a large group of compounds that contain fatty glycerol. Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids. Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, fill numerous roles, such as the storage and transport of energy and structural components; the basic carbohydrate units are called monosaccharides and include galactose and most glucose. Monosaccharides can be linked together to form polysaccharides in limitless ways; the two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group, attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, its interpretation through the processes of transcription and protein biosynthesis.
This information is propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made
Genome projects are scientific endeavours that aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences; the Human Genome Project was a landmark genome project, having a major impact on research across the life sciences, with potential for spurring numerous medical and commercial developments. Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source is first fractured into millions of small pieces.
These pieces are "read" by automated sequencing machines, which can read up to 1000 nucleotides or bases at a time. A genome assembly algorithm works by taking all the pieces and aligning them to one another, detecting all places where two of the short sequences, or reads, overlap; these overlapping reads can be merged, the process continues. Genome assembly is a difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as repeats; these repeats can be thousands of nucleotides long, some occur in thousands of different locations in the large genomes of plants and animals. The resulting genome sequence is produced by combining the information sequenced contigs and employing linking information to create scaffolds. Scaffolds are positioned along the physical map of the chromosomes creating a "golden path". Most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced. However, this has changed as the software has grown more complex and as the number of sequencing centers has increased.
An example of such assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, indel finding, structural variation analysis. Since the 1980s, molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the process of identifying attaching biological information to sequences, in identifying the locations of genes and determining what those genes do; when sequencing a genome, there are regions that are difficult to sequence. Thus,'completed' genome sequences are ever complete, terms such as'working draft' or'essentially complete' have been used to more describe the status of such genome projects; when every base pair of a genome sequence has been determined, there are still to be errors present because DNA sequencing is not a accurate process. It could be argued that a complete genome project should include the sequences of mitochondria and chloroplasts as these organelles have their own genomes.
It is reported that the goal of sequencing a genome is to obtain information about the complete set of genes in that particular genome sequence. The proportion of a genome that encodes for genes may be small. However, it is not always possible to only sequence the coding regions separately; as scientists understand more about the role of this noncoding DNA, it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism. In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism; such projects may include gene prediction to find out where the genes are in a genome, what those genes do. There may be related projects to sequence ESTs or mRNAs to help find out where the genes are; when sequencing eukaryotic genomes it was common to first map the genome to provide a series of landmarks across the genome. Rather than sequence a chromosome in one go, it would be sequenced piece by piece.
Changes in technology and in particular improvements to the processing power of computers, means that genomes can now be'shotgun sequenced' in one go. Improvements in DNA sequencing technology has meant that the cost of sequencing a new genome sequence has fallen and newer technology has meant that genomes can be sequenced far more quickly; when research agencies decide what new genomes to sequence, the emphasis has been on species which are either high importance as model organism or have a relevance to human health or species which have commercial importance. Secondary emphasis is placed on species whose genomes will help answer important questions in molecu
The phenotype of an organism is the composite of the organism's observable characteristics or traits, including its morphology or physical form and structure. An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, the influence of environmental factors, which may interact, further affecting phenotype; when two or more different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented polymorphism is Labrador Retriever coloring. Richard Dawkins in 1978 and again in his 1982 book The Extended Phenotype suggested that bird nests and other built structures such as caddis fly larvae cases and beaver dams can be considered as "extended phenotypes"; the genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm and somatic cells.
The genotype-phenotype distinction should not be confused with Francis Crick's central dogma of molecular biology, a statement about the directionality of molecular sequential information flowing from DNA to protein, not the reverse. The term "phenotype" has sometimes been incorrectly used as a shorthand for phenotypic difference from wild type, bringing the absurd statement that a mutation has no phenotype. Despite its straightforward definition, the concept of the phenotype has hidden subtleties, it may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable and are thus part of the phenotype, it may seem that this goes beyond the original intentions of the concept with its focus on the organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits that can be made visible by some technical procedure.
A notable extension to this idea is the presence of "organic molecules" or metabolites that are generated by organisms from chemical reactions of enzymes. Another extension adds behavior to the phenotype. Behavioral phenotypes include cognitive and behavioral patterns; some behavioral phenotypes may characterize psychiatric syndromes. Phenotypic variation is a fundamental prerequisite for evolution by natural selection, it is the living organism as a whole that contributes to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection; the interaction between genotype and phenotype has been conceptualized by the following relationship: genotype + environment → phenotype A more nuanced version of the relationship is: genotype + environment + genotype & environment interactions → phenotype Genotypes have much flexibility in the modification and expression of phenotypes.
The plant Hieracium umbellatum is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy with broad leaves and expanded inflorescences; these habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine the phenotype that grows. An example of random variation in Drosophila flies is the number of ommatidia, which may vary between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments; the concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, silent mutations that do not change the corresponding amino acid sequence of a gene may change the frequency of guanine-cytosine base pairs; these base pairs have a higher thermal stability than adenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.
Richard Dawkins described a phenotype that included all effects that a gene has on its surroundings, including other organisms, as an extended phenotype, arguing that "An animal's behavior tends to maximize the survival of the genes'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it." For instance, an organism such as a beaver modifies its environment by building a beaver dam. When a bird feeds a brood parasite such as a cuckoo, it is unwittingly extending its phenotype.
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis; as a consequence, the DNA repair process is active as it responds to damage in the DNA structure. When normal repair processes fail, when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and DNA crosslinkages; this can lead to malignant tumors, or cancer as per the two hit hypothesis. The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, the extracellular environment.
A cell that has accumulated a large amount of DNA damage, or one that no longer repairs damage incurred to its DNA, can enter one of three possible states: an irreversible state of dormancy, known as senescence cell suicide known as apoptosis or programmed cell death unregulated cell division, which can lead to the formation of a tumor, cancerousThe DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal functionality of that organism. Many genes that were shown to influence life span have turned out to be involved in DNA damage repair and protection; the 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich, Aziz Sancar for their work on the molecular mechanisms of DNA repair processes. DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome's 6 billion bases, unrepaired lesions in critical genes can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation and contribute to tumour heterogeneity.
The vast majority of DNA damage affects the primary structure of the double helix. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however and wound around "packaging" proteins called histones, both superstructures are vulnerable to the effects of DNA damage. DNA damage can be subdivided into two main types: endogenous damage such as attack by reactive oxygen species produced from normal metabolic byproducts the process of oxidative deamination includes replication errors exogenous damage caused by external agents such as ultraviolet radiation from the sun other radiation frequencies, including x-rays and gamma rays hydrolysis or thermal disruption certain plant toxins human-made mutagenic chemicals aromatic compounds that act as DNA intercalating agents virusesThe replication of damaged DNA before cell division can lead to the incorporation of wrong bases opposite damaged ones.
Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable. There are several types of damage to DNA due to endogenous cellular processes: oxidation of bases and generation of DNA strand interruptions from reactive oxygen species, alkylation of bases, such as formation of 7-methylguanosine, 1-methyladenine, 6-O-Methylguanine hydrolysis of bases, such as deamination and depyrimidination. "bulky adduct formation" mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is stitched into place in a newly forming DNA strand, or a DNA base is skipped over or mistakenly inserted. Monoadduct damage cause by change in single nitrogenous base of DNA Diadduct damageDamage caused by exogenous agents comes in many forms; some examples are: UV-B light causes crosslinking between adjacent cytosine and thymine bases creating pyrimidine dimers. This is called direct DNA damage. UV-A light creates free radicals; the damage caused by free radicals is called indirect DNA damage.
Ionizing radiation such as that created by radioactive decay or in cosmic rays causes breaks in DNA strands. Intermediate-level ionizing radiation may induce irreparable DNA damage leading to pre-mature aging and cancer. Thermal disruption at elevated temperature increases the rate of depurination and single-strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, which grow in hot springs at 40–80 °C; the rate of depurination is too high in these species to be repaired by normal repair machinery, hence a possibility of an adaptive response cannot be ruled out. Industrial chemicals such as vinyl chloride and hydrogen peroxide, environmental chemicals such as polycyclic
A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and breaking of chemical bonds between atoms, with no change to the nuclei, can be described by a chemical equation. Nuclear chemistry is a sub-discipline of chemistry that involves the chemical reactions of unstable and radioactive elements where both electronic and nuclear changes can occur; the substance involved in a chemical reaction are called reactants or reagents. Chemical reactions are characterized by a chemical change, they yield one or more products, which have properties different from the reactants. Reactions consist of a sequence of individual sub-steps, the so-called elementary reactions, the information on the precise course of action is part of the reaction mechanism. Chemical reactions are described with chemical equations, which symbolically present the starting materials, end products, sometimes intermediate products and reaction conditions.
Chemical reactions happen at a characteristic reaction rate at a given temperature and chemical concentration. Reaction rates increase with increasing temperature because there is more thermal energy available to reach the activation energy necessary for breaking bonds between atoms. Reactions may proceed in the forward or reverse direction until they go to completion or reach equilibrium. Reactions that proceed in the forward direction to approach equilibrium are described as spontaneous, requiring no input of free energy to go forward. Non-spontaneous reactions require input of free energy to go forward. Different chemical reactions are used in combinations during chemical synthesis in order to obtain a desired product. In biochemistry, a consecutive series of chemical reactions form metabolic pathways; these reactions are catalyzed by protein enzymes. Enzymes increase the rates of biochemical reactions, so that metabolic syntheses and decompositions impossible under ordinary conditions can occur at the temperatures and concentrations present within a cell.
The general concept of a chemical reaction has been extended to reactions between entities smaller than atoms, including nuclear reactions, radioactive decays, reactions between elementary particles, as described by quantum field theory. Chemical reactions such as combustion in fire and the reduction of ores to metals were known since antiquity. Initial theories of transformation of materials were developed by Greek philosophers, such as the Four-Element Theory of Empedocles stating that any substance is composed of the four basic elements – fire, water and earth. In the Middle Ages, chemical transformations were studied by Alchemists, they attempted, in particular, to convert lead into gold, for which purpose they used reactions of lead and lead-copper alloys with sulfur. The production of chemical substances that do not occur in nature has long been tried, such as the synthesis of sulfuric and nitric acids attributed to the controversial alchemist Jābir ibn Hayyān; the process involved heating of sulfate and nitrate minerals such as copper sulfate and saltpeter.
In the 17th century, Johann Rudolph Glauber produced hydrochloric acid and sodium sulfate by reacting sulfuric acid and sodium chloride. With the development of the lead chamber process in 1746 and the Leblanc process, allowing large-scale production of sulfuric acid and sodium carbonate chemical reactions became implemented into the industry. Further optimization of sulfuric acid technology resulted in the contact process in the 1880s, the Haber process was developed in 1909–1910 for ammonia synthesis. From the 16th century, researchers including Jan Baptist van Helmont, Robert Boyle, Isaac Newton tried to establish theories of the experimentally observed chemical transformations; the phlogiston theory was proposed in 1667 by Johann Joachim Becher. It postulated the existence of a fire-like element called "phlogiston", contained within combustible bodies and released during combustion; this proved to be false in 1785 by Antoine Lavoisier who found the correct explanation of the combustion as reaction with oxygen from the air.
Joseph Louis Gay-Lussac recognized in 1808 that gases always react in a certain relationship with each other. Based on this idea and the atomic theory of John Dalton, Joseph Proust had developed the law of definite proportions, which resulted in the concepts of stoichiometry and chemical equations. Regarding the organic chemistry, it was long believed that compounds obtained from living organisms were too complex to be obtained synthetically. According to the concept of vitalism, organic matter was endowed with a "vital force" and distinguished from inorganic materials; this separation was ended however by the synthesis of urea from inorganic precursors by Friedrich Wöhler in 1828. Other chemists who brought major contributions to organic chemistry include Alexander William Williamson with his synthesis of ethers and Christopher Kelk Ingold, among many discoveries, established the mechanisms of substitution reactions. Chemical equations are used to graphically illustrate chemical reactions, they consist of chemical or structural formulas of the reactants on the left and those of the products on the right.
They are separated by an arrow which indicates the type of the reaction.
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may 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 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. Recent studies use either "shotgun" or PCR directed sequencing to get unbiased samples of all genes from all the members of the sampled communities; because of its ability to reveal the hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.
The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F. Brady, others, 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. In 2005, Kevin Chen and Lior Pachter defined metagenomics as "the application of modern genomics technique without the need for isolation and lab cultivation of individual species". Conventional sequencing begins with a culture of identical cells as a source of DNA. However, early metagenomic studies revealed that there are large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced; these early studies focused on 16S ribosomal RNA sequences which are short conserved within a species, different between species. Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous non-isolated organisms.
These surveys of ribosomal RNA genes taken directly from the environment revealed that cultivation based methods find less than 1% of the bacterial and archaeal species in a sample. Much of the interest in metagenomics comes from these discoveries that showed that the vast majority of microorganisms had gone unnoticed. Early molecular work in the field was conducted by Norman R. Pace and colleagues, who used PCR to explore the diversity of ribosomal RNA sequences; the insights gained from these breakthrough studies led Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985. This led to the first report of isolating and cloning bulk DNA from an environmental sample, published by Pace and colleagues in 1991 while Pace was in the Department of Biology at Indiana University. Considerable efforts ensured that these were not PCR false positives and supported the existence of a complex community of unexplored species. Although this methodology was limited to exploring conserved, non-protein coding genes, it did support early microbial morphology-based observations that diversity was far more complex than was known by culturing methods.
Soon after that, Healy reported the metagenomic isolation of functional genes from "zoolibraries" constructed from a complex culture of environmental organisms grown in the laboratory on dried grasses in 1995. After leaving the Pace laboratory, Edward DeLong continued in the field and has published work that has laid the groundwork for environmental phylogenies based on signature 16S sequences, beginning with his group's construction of libraries from marine samples. In 2002, Mya Breitbart, Forest Rohwer, colleagues used environmental shotgun sequencing to show that 200 liters of seawater contains over 5000 different viruses. Subsequent studies showed that there are more than a thousand viral species in human stool and a million different viruses per kilogram of marine sediment, including many bacteriophages. All of the viruses in these studies were new species. In 2004, Gene Tyson, Jill Banfield, colleagues at the University of California and the Joint Genome Institute sequenced DNA extracted from an acid mine drainage system.
This effort resulted in the complete, or nearly complete, genomes for a handful of bacteria and archaea that had resisted attempts to culture them. Beginning in 2003, Craig Venter, leader of the funded parallel of the Human Genome Project, has led the Global Ocean Sampling Expedition, circumnavigating the globe and collecting metagenomic samples throughout the journey. All of these samples are sequenced using shotgun sequencing, in hopes that new genomes would be identified; the pilot project, conducted in the Sargasso Sea, found DNA from nearly 2000 different species, including 148 types of bacteria never before seen. Venter has circumnavigated the globe and explored the West Coast of the United States, completed a two-year expedition to explore the Baltic and Black Seas. Analysis of the metagenomic data collected during this journey revealed two groups of organisms, one composed of taxa adapted to environmental conditions of'feast or famine', a second composed of fewer but more abundantly and distributed taxa composed of plankton.
In 2005 Stephan C. Schuster at Penn State University and colleagues published the first sequences of an environmental sample generated with high-throughput sequencing, in this case massively parallel pyrosequencing developed by 454 Life Sciences. Another early paper in t
In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA; the genome includes both the genes and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics; the term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words chromosome. However, see omics for a more thorough discussion. A few related -ome words existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically. A genome sequence is the complete list of the nucleotides that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete nucleotide sequence of a viral RNA-genome.
The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs. The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s; the first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made genome sequencing cheaper and easier, the number of complete genome sequences is growing rapidly; the US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, the bacteria E. coli.
In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave. New sequencing technologies, such as massive parallel sequencing have opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than aids in navigating around the genome; the Human Genome Project was organized to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.
The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA. LAND at the New York Genome Center, an example both of the economies of scale and of citizen science. Viral genomes can be composed of either RNA or DNA; the genomes of RNA viruses can be either single-stranded or double-stranded RNA, may contain one or more separate RNA molecules. DNA viruses can have either double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea have a single circular chromosome. Most bacteria have a single circular chromosome. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, if the cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and partially replicated chromosomes.
Most prokaryotes have little repetitive DNA in their genomes. However, some symbiotic bacteria have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins; some bacteria have auxiliary genetic material part of their genome, carried in plasmids. For this, the word genome should not be used as a synonym of chromosome. Eukaryotic genomes are composed of one or more linear DNA chromosomes; the number of chromosomes varies from Jack jumper ants and an asexual nemotode, which each have only one pair, to a fern species that has 720 pairs. A typical human cell has two copies of each of 22 autosomes, one inherited from each parent, plus two sex chromosomes, making it diploid. Gametes, such as ova, sperm and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to the chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome referred to as the "mitochondrial genome".
The DNA found within the chloroplast may be referred to as the "plastome". Like the bacteria they originated from and chloroplasts have a circular chromosome