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129-588: Franz Georg Philipp Buchenau (12 January 1831 – 23 April 1906) was a German botanist and phytogeographer who was a native of Kassel . He specialized in flora of northwestern Germany. He studied at the Universities of Marburg and Göttingen , and from 1855 was a schoolteacher in Bremen . In 1864 he was co-founder of the association for natural sciences in Bremen. Buchenau was the author of works involving

258-479: A 3'- OH group required for the formation of a phosphodiester bond between two nucleotides, causing DNA polymerase to cease extension of DNA when a ddNTP is incorporated. The ddNTPs may be radioactively or fluorescently labelled for detection in DNA sequencers . Typically, these machines can sequence up to 96 DNA samples in a single batch (run) in up to 48 runs a day. The high demand for low-cost sequencing has driven

387-642: A Preventive Genomics Clinic in August 2019, with Massachusetts General Hospital following a month later. The All of Us research program aims to collect genome sequence data from 1 million participants to become a critical component of the precision medicine research platform and the UK Biobank initiative has studied more than 500.000 individuals with deep genomic and phenotypic data. The growth of genomic knowledge has enabled increasingly sophisticated applications of synthetic biology . In 2010 researchers at

516-517: A base is incorporated. A microwell containing template DNA is flooded with a single nucleotide , if the nucleotide is complementary to the template strand it will be incorporated and a hydrogen ion will be released. This release triggers an ISFET ion sensor. If a homopolymer is present in the template sequence multiple nucleotides will be incorporated in a single flood cycle, and the detected electrical signal will be proportionally higher. Sequence assembly refers to aligning and merging fragments of

645-490: A botanically and pharmacologically important herbal Historia Plantarum in 1544 and a pharmacopoeia of lasting importance, the Dispensatorium in 1546. Naturalist Conrad von Gesner (1516–1565) and herbalist John Gerard (1545– c.  1611 ) published herbals covering the supposed medicinal uses of plants. Naturalist Ulisse Aldrovandi (1522–1605) was considered the father of natural history , which included

774-467: A combination of experimental and modeling approaches . The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because

903-414: A considerable problem in agriculture, and the biology and control of plant pathogens in agriculture and natural ecosystems . Ethnobotany is the study of the relationships between plants and people. When applied to the investigation of historical plant–people relationships ethnobotany may be referred to as archaeobotany or palaeoethnobotany . Some of the earliest plant-people relationships arose between

1032-452: A continuum between the major morphological categories of root, stem (caulome), leaf (phyllome) and trichome . Furthermore, it emphasises structural dynamics. Modern systematics aims to reflect and discover phylogenetic relationships between plants. Modern Molecular phylogenetics largely ignores morphological characters, relying on DNA sequences as data. Molecular analysis of DNA sequences from most families of flowering plants enabled

1161-464: A eukaryote, S. cerevisiae (12.1 Mb), and since then genomes have continued being sequenced at an exponentially growing pace. As of October 2011 , the complete sequences are available for: 2,719 viruses , 1,115 archaea and bacteria , and 36 eukaryotes , of which about half are fungi . Most of the microorganisms whose genomes have been completely sequenced are problematic pathogens , such as Haemophilus influenzae , which has resulted in

1290-451: A field of study in biology ending in -omics , such as genomics, proteomics or metabolomics . The related suffix -ome is used to address the objects of study of such fields, such as the genome , proteome , or metabolome ( lipidome ) respectively. The suffix -ome as used in molecular biology refers to a totality of some sort; similarly omics has come to refer generally to the study of large, comprehensive biological data sets. While

1419-501: A global level has been made possible only recently through the adaptation of genomic high-throughput assays. Metagenomics is the study of metagenomes , 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 rely upon cultivated clonal cultures , early environmental gene sequencing cloned specific genes (often

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1548-400: A hierarchical classification of plant species that remains the reference point for modern botanical nomenclature . This established a standardised binomial or two-part naming scheme where the first name represented the genus and the second identified the species within the genus. For the purposes of identification, Linnaeus's Systema Sexuale classified plants into 24 groups according to

1677-408: A high error rate at approximately 1 percent. Typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcripts ( ESTs ). Assembly can be broadly categorized into two approaches: de novo assembly, for genomes which are not similar to any sequenced in the past, and comparative assembly, which uses the existing sequence of a closely related organism as

1806-427: A much longer DNA sequence in order to reconstruct the original sequence. This is needed as current DNA sequencing technology cannot read whole genomes as a continuous sequence, but rather reads small pieces of between 20 and 1000 bases, depending on the technology used. Third generation sequencing technologies such as PacBio or Oxford Nanopore routinely generate sequencing reads 10-100 kb in length; however, they have

1935-404: A plant sucks water through them under water stress. Lignin is also used in other cell types like sclerenchyma fibres that provide structural support for a plant and is a major constituent of wood. Sporopollenin is a chemically resistant polymer found in the outer cell walls of spores and pollen of land plants responsible for the survival of early land plant spores and the pollen of seed plants in

2064-552: A polymer of fructose is used for the same purpose in the sunflower family Asteraceae . Some of the glucose is converted to sucrose (common table sugar) for export to the rest of the plant. Unlike in animals (which lack chloroplasts), plants and their eukaryote relatives have delegated many biochemical roles to their chloroplasts , including synthesising all their fatty acids , and most amino acids . The fatty acids that chloroplasts make are used for many things, such as providing material to build cell membranes out of and making

2193-464: A process that generates molecular oxygen (O 2 ) as a by-product. The light energy captured by chlorophyll a is initially in the form of electrons (and later a proton gradient ) that's used to make molecules of ATP and NADPH which temporarily store and transport energy. Their energy is used in the light-independent reactions of the Calvin cycle by the enzyme rubisco to produce molecules of

2322-499: A pronounced bias in their phylogenetic distribution compared to the breadth of microbial diversity. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models. Yeast ( Saccharomyces cerevisiae ) has long been an important model organism for the eukaryotic cell , while the fruit fly Drosophila melanogaster has been a very important tool (notably in early pre-molecular genetics ). The worm Caenorhabditis elegans

2451-475: A protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure. As opposed to traditional structural biology , the determination of a protein structure through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. This raises new challenges in structural bioinformatics , i.e. determining protein function from its 3D structure. Epigenomics

2580-505: A pure form of carbon made by pyrolysis of wood, has a long history as a metal- smelting fuel, as a filter material and adsorbent and as an artist's material and is one of the three ingredients of gunpowder . Cellulose , the world's most abundant organic polymer, can be converted into energy, fuels, materials and chemical feedstock. Products made from cellulose include rayon and cellophane , wallpaper paste , biobutanol and gun cotton . Sugarcane , rapeseed and soy are some of

2709-515: A range of software tools in their automated genome annotation pipeline. Structural annotation consists of the identification of genomic elements, primarily ORFs and their localisation, or gene structure. Functional annotation consists of attaching biological information to genomic elements. The need for reproducibility and efficient management of the large amount of data associated with genome projects mean that computational pipelines have important applications in genomics. Functional genomics

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2838-432: A reference during assembly. Relative to comparative assembly, de novo assembly is computationally difficult ( NP-hard ), making it less favourable for short-read NGS technologies. Within the de novo assembly paradigm there are two primary strategies for assembly, Eulerian path strategies, and overlap-layout-consensus (OLC) strategies. OLC strategies ultimately try to create a Hamiltonian path through an overlap graph which

2967-499: A sequencing procedure using DNA polymerase with radiolabelled nucleotides that he called the Plus and Minus technique . This involved two closely related methods that generated short oligonucleotides with defined 3' termini. These could be fractionated by electrophoresis on a polyacrylamide gel (called polyacrylamide gel electrophoresis) and visualised using autoradiography. The procedure could sequence up to 80 nucleotides in one go and

3096-536: A student of Aristotle who invented and described many of its principles and is widely regarded in the scientific community as the "Father of Botany". His major works, Enquiry into Plants and On the Causes of Plants , constitute the most important contributions to botanical science until the Middle Ages , almost seventeen centuries later. Another work from Ancient Greece that made an early impact on botany

3225-434: A substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome: Overall, this method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes. At present there are 24 cyanobacteria for which

3354-628: A total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six Prochlorococcus strains, seven marine Synechococcus strains, Trichodesmium erythraeum IMS101 and Crocosphaera watsonii WH8501 . Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further Prochlorococcus and marine Synechococcus isolates, Acaryochloris and Prochloron ,

3483-460: A useful proxy for temperature in historical climatology , and the biological impact of climate change and global warming . Palynology , the analysis of fossil pollen deposits in sediments from thousands or millions of years ago allows the reconstruction of past climates. Estimates of atmospheric CO 2 concentrations since the Palaeozoic have been obtained from stomatal densities and

3612-1010: A variety of spatial scales in groups, populations and communities that collectively constitute vegetation. Regions with characteristic vegetation types and dominant plants as well as similar abiotic and biotic factors, climate , and geography make up biomes like tundra or tropical rainforest . Herbivores eat plants, but plants can defend themselves and some species are parasitic or even carnivorous . Other organisms form mutually beneficial relationships with plants. For example, mycorrhizal fungi and rhizobia provide plants with nutrients in exchange for food, ants are recruited by ant plants to provide protection, honey bees , bats and other animals pollinate flowers and humans and other animals act as dispersal vectors to spread spores and seeds . Plant responses to climate and other environmental changes can inform our understanding of how these changes affect ecosystem function and productivity. For example, plant phenology can be

3741-628: A way of drug discovery . Plants can synthesise coloured dyes and pigments such as the anthocyanins responsible for the red colour of red wine , yellow weld and blue woad used together to produce Lincoln green , indoxyl , source of the blue dye indigo traditionally used to dye denim and the artist's pigments gamboge and rose madder . Sugar, starch , cotton, linen , hemp , some types of rope , wood and particle boards , papyrus and paper, vegetable oils , wax , and natural rubber are examples of commercially important materials made from plant tissues or their secondary products. Charcoal ,

3870-456: A wider range of shared characters and were widely followed. The Candollean system reflected his ideas of the progression of morphological complexity and the later Bentham & Hooker system , which was influential until the mid-19th century, was influenced by Candolle's approach. Darwin 's publication of the Origin of Species in 1859 and his concept of common descent required modifications to

3999-499: A year, to local molecular biology core facilities) which contain research laboratories with the costly instrumentation and technical support necessary. As sequencing technology continues to improve, however, a new generation of effective fast turnaround benchtop sequencers has come within reach of the average academic laboratory. On the whole, genome sequencing approaches fall into two broad categories, shotgun and high-throughput (or next-generation ) sequencing. Shotgun sequencing

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4128-406: Is De materia medica , a five-volume encyclopedia about preliminary herbal medicine written in the middle of the first century by Greek physician and pharmacologist Pedanius Dioscorides . De materia medica was widely read for more than 1,500 years. Important contributions from the medieval Muslim world include Ibn Wahshiyya 's Nabatean Agriculture , Abū Ḥanīfa Dīnawarī 's (828–896)

4257-405: Is peppermint , Mentha × piperita , a sterile hybrid between Mentha aquatica and spearmint, Mentha spicata . The many cultivated varieties of wheat are the result of multiple inter- and intra- specific crosses between wild species and their hybrids. Angiosperms with monoecious flowers often have self-incompatibility mechanisms that operate between the pollen and stigma so that

4386-476: Is a broad, multidisciplinary subject with contributions and insights from most other areas of science and technology. Research topics include the study of plant structure , growth and differentiation, reproduction , biochemistry and primary metabolism , chemical products, development , diseases , evolutionary relationships , systematics , and plant taxonomy . Dominant themes in 21st-century plant science are molecular genetics and epigenetics , which study

4515-502: Is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects ) to describe gene (and protein ) functions and interactions. Functional genomics focuses on the dynamic aspects such as gene transcription , translation , and protein–protein interactions , as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about

4644-471: Is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a shotgun . Since gel electrophoresis sequencing can only be used for fairly short sequences (100 to 1000 base pairs), longer DNA sequences must be broken into random small segments which are then sequenced to obtain reads . Multiple overlapping reads for

4773-732: Is an NP-hard problem. Eulerian path strategies are computationally more tractable because they try to find a Eulerian path through a deBruijn graph. Finished genomes are defined as having a single contiguous sequence with no ambiguities representing each replicon . The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching biological information to sequences , and consists of three main steps: Automatic annotation tools try to perform these steps in silico , as opposed to manual annotation (a.k.a. curation) which involves human expertise and potential experimental verification. Ideally, these approaches co-exist and complement each other in

4902-697: Is an often used simple model for multicellular organisms . The zebrafish Brachydanio rerio is used for many developmental studies on the molecular level, and the plant Arabidopsis thaliana is a model organism for flowering plants. The Japanese pufferfish ( Takifugu rubripes ) and the spotted green pufferfish ( Tetraodon nigroviridis ) are interesting because of their small and compact genomes, which contain very little noncoding DNA compared to most species. The mammals dog ( Canis familiaris ), brown rat ( Rattus norvegicus ), mouse ( Mus musculus ), and chimpanzee ( Pan troglodytes ) are all important model animals in medical research. A rough draft of

5031-587: Is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical Research Institute, by Pascal Mayer and Laurent Farinelli. In this method, DNA molecules and primers are first attached on a slide and amplified with polymerase so that local clonal colonies, initially coined "DNA colonies", are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. Unlike pyrosequencing,

5160-762: Is gathered by ethnobotanists. This information can relay a great deal of information on how the land once was thousands of years ago and how it has changed over that time. The goals of plant ecology are to understand the causes of their distribution patterns, productivity, environmental impact, evolution, and responses to environmental change. Plants depend on certain edaphic (soil) and climatic factors in their environment but can modify these factors too. For example, they can change their environment's albedo , increase runoff interception, stabilise mineral soils and develop their organic content, and affect local temperature. Plants compete with other organisms in their ecosystem for resources. They interact with their neighbours at

5289-486: Is over-sampled is referred to as coverage . For much of its history, the technology underlying shotgun sequencing was the classical chain-termination method or ' Sanger method ', which is based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication . Recently, shotgun sequencing has been supplanted by high-throughput sequencing methods, especially for large-scale, automated genome analyses. However,

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5418-451: Is still a major foundation of modern botany. Her books Plant Anatomy and Anatomy of Seed Plants have been key plant structural biology texts for more than half a century. The discipline of plant ecology was pioneered in the late 19th century by botanists such as Eugenius Warming , who produced the hypothesis that plants form communities , and his mentor and successor Christen C. Raunkiær whose system for describing plant life forms

5547-400: Is still given to these groups by botanists, and fungi (including lichens) and photosynthetic protists are usually covered in introductory botany courses. Palaeobotanists study ancient plants in the fossil record to provide information about the evolutionary history of plants . Cyanobacteria , the first oxygen-releasing photosynthetic organisms on Earth, are thought to have given rise to

5676-444: Is still in use today. The concept that the composition of plant communities such as temperate broadleaf forest changes by a process of ecological succession was developed by Henry Chandler Cowles , Arthur Tansley and Frederic Clements . Clements is credited with the idea of climax vegetation as the most complex vegetation that an environment can support and Tansley introduced the concept of ecosystems to biology. Building on

5805-502: Is the science of plant life and a branch of biology . A botanist , plant scientist or phytologist is a scientist who specialises in this field. The term "botany" comes from the Ancient Greek word botanē ( βοτάνη ) meaning " pasture ", " herbs " " grass ", or " fodder "; Botanē is in turn derived from boskein ( Greek : βόσκειν ), "to feed" or "to graze ". Traditionally, botany has also included

5934-498: Is the study of ferns and allied plants. A number of other taxa of ranks varying from family to subgenus have terms for their study, including agrostology (or graminology) for the study of grasses, synantherology for the study of composites, and batology for the study of brambles. Study can also be divided by guild rather than clade or grade . Dendrology is the study of woody plants. Many divisions of biology have botanical subfields. These are commonly denoted by prefixing

6063-679: Is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome . Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p. 475). Two of the most characterized epigenetic modifications are DNA methylation and histone modification . Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis . The study of epigenetics on

6192-411: 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. Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its power to reveal

6321-564: The Angiosperm Phylogeny Group to publish in 1998 a phylogeny of flowering plants, answering many of the questions about relationships among angiosperm families and species. The theoretical possibility of a practical method for identification of plant species and commercial varieties by DNA barcoding is the subject of active current research. Botany is divided along several axes. Some subfields of botany relate to particular groups of organisms. Divisions related to

6450-499: The Book of Plants , and Ibn Bassal 's The Classification of Soils . In the early 13th century, Abu al-Abbas al-Nabati , and Ibn al-Baitar (d. 1248) wrote on botany in a systematic and scientific manner. In the mid-16th century, botanical gardens were founded in a number of Italian universities. The Padua botanical garden in 1545 is usually considered to be the first which is still in its original location. These gardens continued

6579-417: The C 4 carbon fixation pathway for photosynthesis which avoid the losses resulting from photorespiration in the more common C 3 carbon fixation pathway. These biochemical strategies are unique to land plants. Phytochemistry is a branch of plant biochemistry primarily concerned with the chemical substances produced by plants during secondary metabolism . Some of these compounds are toxins such as

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6708-633: The J. Craig Venter Institute announced the creation of a partially synthetic species of bacterium , Mycoplasma laboratorium , derived from the genome of Mycoplasma genitalium . Population genomics has developed as a popular field of research, where genomic sequencing methods are used to conduct large-scale comparisons of DNA sequences among populations - beyond the limits of genetic markers such as short-range PCR products or microsatellites traditionally used in population genetics . Population genomics studies genome -wide effects to improve our understanding of microevolution so that we may learn

6837-525: The Jackson Laboratory ( Bar Harbor, Maine ), over beers with Jim Womack, Tom Shows and Stephen O’Brien at a meeting held in Maryland on the mapping of the human genome in 1986. First as the name for a new journal and then as a whole new science discipline. Following Rosalind Franklin 's confirmation of the helical structure of DNA, James D. Watson and Francis Crick 's publication of

6966-504: The alkaloid coniine from hemlock . Others, such as the essential oils peppermint oil and lemon oil are useful for their aroma, as flavourings and spices (e.g., capsaicin ), and in medicine as pharmaceuticals as in opium from opium poppies . Many medicinal and recreational drugs , such as tetrahydrocannabinol (active ingredient in cannabis ), caffeine , morphine and nicotine come directly from plants. Others are simple derivatives of botanical natural products. For example,

7095-565: The auxin plant hormones by Kenneth V. Thimann in 1948 enabled regulation of plant growth by externally applied chemicals. Frederick Campion Steward pioneered techniques of micropropagation and plant tissue culture controlled by plant hormones . The synthetic auxin 2,4-dichlorophenoxyacetic acid or 2,4-D was one of the first commercial synthetic herbicides . 20th century developments in plant biochemistry have been driven by modern techniques of organic chemical analysis , such as spectroscopy , chromatography and electrophoresis . With

7224-626: The cell theory with Theodor Schwann and Rudolf Virchow and was among the first to grasp the significance of the cell nucleus that had been described by Robert Brown in 1831. In 1855, Adolf Fick formulated Fick's laws that enabled the calculation of the rates of molecular diffusion in biological systems. Building upon the gene-chromosome theory of heredity that originated with Gregor Mendel (1822–1884), August Weismann (1834–1914) proved that inheritance only takes place through gametes . No other cells can pass on inherited characters. The work of Katherine Esau (1898–1997) on plant anatomy

7353-444: The cellulose and lignin used to build their bodies, and secondary products like resins and aroma compounds . Plants and various other groups of photosynthetic eukaryotes collectively known as " algae " have unique organelles known as chloroplasts . Chloroplasts are thought to be descended from cyanobacteria that formed endosymbiotic relationships with ancient plant and algal ancestors. Chloroplasts and cyanobacteria contain

7482-475: The human genome was completed by the Human Genome Project in early 2001, creating much fanfare. This project, completed in 2003, sequenced the entire genome for one specific person, and by 2007 this sequence was declared "finished" (less than one error in 20,000 bases and all chromosomes assembled). In the years since then, the genomes of many other individuals have been sequenced, partly under

7611-427: The indigenous people of Canada in identifying edible plants from inedible plants. This relationship the indigenous people had with plants was recorded by ethnobotanists. Plant biochemistry is the study of the chemical processes used by plants. Some of these processes are used in their primary metabolism like the photosynthetic Calvin cycle and crassulacean acid metabolism . Others make specialised materials like

7740-442: The phylogenetic history and demography of a population. Population genomic methods are used for many different fields including evolutionary biology , ecology , biogeography , conservation biology and fisheries management . Similarly, landscape genomics has developed from landscape genetics to use genomic methods to identify relationships between patterns of environmental and genetic variation. Conservationists can use

7869-426: The pines , and flowering plants ) and the free-sporing cryptogams including ferns , clubmosses , liverworts , hornworts and mosses . Embryophytes are multicellular eukaryotes descended from an ancestor that obtained its energy from sunlight by photosynthesis . They have life cycles with alternating haploid and diploid phases. The sexual haploid phase of embryophytes, known as the gametophyte , nurtures

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7998-439: The 1980 Nobel Prize in chemistry with Paul Berg ( recombinant DNA ). The advent of these technologies resulted in a rapid intensification in the scope and speed of completion of genome sequencing projects . The first complete genome sequence of a eukaryotic organelle , the human mitochondrion (16,568 bp, about 16.6 kb [kilobase]), was reported in 1981, and the first chloroplast genomes followed in 1986. In 1992,

8127-408: The 3-carbon sugar glyceraldehyde 3-phosphate (G3P). Glyceraldehyde 3-phosphate is the first product of photosynthesis and the raw material from which glucose and almost all other organic molecules of biological origin are synthesised. Some of the glucose is converted to starch which is stored in the chloroplast. Starch is the characteristic energy store of most land plants and algae, while inulin ,

8256-517: The Candollean system to reflect evolutionary relationships as distinct from mere morphological similarity. Botany was greatly stimulated by the appearance of the first "modern" textbook, Matthias Schleiden 's Grundzüge der Wissenschaftlichen Botanik , published in English in 1849 as Principles of Scientific Botany . Schleiden was a microscopist and an early plant anatomist who co-founded

8385-416: The DNA chains are extended one nucleotide at a time and image acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera. Decoupling the enzymatic reaction and the image capture allows for optimal throughput and theoretically unlimited sequencing capacity; with an optimal configuration, the ultimate throughput of

8514-449: The N 2 -fixing filamentous cyanobacteria Nodularia spumigena , Lyngbya aestuarii and Lyngbya majuscula , as well as bacteriophages infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights into

8643-481: The Sanger method remains in wide use, primarily for smaller-scale projects and for obtaining especially long contiguous DNA sequence reads (>500 nucleotides). Chain-termination methods require a single-stranded DNA template, a DNA primer , a DNA polymerase , normal deoxynucleosidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation. These chain-terminating nucleotides lack

8772-482: The Vegetable Kingdom at the start of chapter XII noted "The first and most important of the conclusions which may be drawn from the observations given in this volume, is that generally cross-fertilisation is beneficial and self-fertilisation often injurious, at least with the plants on which I experimented." An important adaptive benefit of outcrossing is that it allows the masking of deleterious mutations in

8901-412: The above pair of categories gives rise to fields such as bryogeography (the study of the distribution of mosses). Different parts of plants also give rise to their own subfields, including xylology , carpology (or fructology) and palynology , these been the study of wood, fruit and pollen/spores respectively. Botany also overlaps on the one hand with agriculture, horticulture and silviculture, and on

9030-439: The ancestor of plants by entering into an endosymbiotic relationship with an early eukaryote, ultimately becoming the chloroplasts in plant cells. The new photosynthetic plants (along with their algal relatives) accelerated the rise in atmospheric oxygen started by the cyanobacteria , changing the ancient oxygen-free, reducing , atmosphere to one in which free oxygen has been abundant for more than 2 billion years. Among

9159-575: The auspices of the 1000 Genomes Project , which announced the sequencing of 1,092 genomes in October 2012. Completion of this project was made possible by the development of dramatically more efficient sequencing technologies and required the commitment of significant bioinformatics resources from a large international collaboration. The continued analysis of human genomic data has profound political and social repercussions for human societies. The English-language neologism omics informally refers to

9288-411: The availability of large numbers of sequenced genomes and previously solved protein structures allow scientists to model protein structure on the structures of previously solved homologs. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to

9417-447: The base of most food chains because they use the energy from the sun and nutrients from the soil and atmosphere, converting them into a form that can be used by animals. This is what ecologists call the first trophic level . The modern forms of the major staple foods , such as hemp , teff , maize, rice, wheat and other cereal grasses, pulses , bananas and plantains, as well as hemp , flax and cotton grown for their fibres, are

9546-500: The blue-green pigment chlorophyll a . Chlorophyll a (as well as its plant and green algal-specific cousin chlorophyll b ) absorbs light in the blue-violet and orange/red parts of the spectrum while reflecting and transmitting the green light that we see as the characteristic colour of these organisms. The energy in the red and blue light that these pigments absorb is used by chloroplasts to make energy-rich carbon compounds from carbon dioxide and water by oxygenic photosynthesis ,

9675-446: The broader historical sense of botany include bacteriology , mycology (or fungology) and phycology - the study of bacteria, fungi and algae respectively - with lichenology as a subfield of mycology. The narrower sense of botany in the sense of the study of embryophytes (land plants) is disambiguated as phytology. Bryology is the study of mosses (and in the broader sense also liverworts and hornworts). Pteridology (or filicology)

9804-513: The characters may be artificial in keys designed purely for identification ( diagnostic keys ) or more closely related to the natural or phyletic order of the taxa in synoptic keys. By the 18th century, new plants for study were arriving in Europe in increasing numbers from newly discovered countries and the European colonies worldwide. In 1753, Carl Linnaeus published his Species Plantarum ,

9933-479: The complete nucleotide-sequence of bacteriophage MS2-RNA (whose genome encodes just four genes in 3569 base pairs [bp]) and Simian virus 40 in 1976 and 1978, respectively. In addition to his seminal work on the amino acid sequence of insulin, Frederick Sanger and his colleagues played a key role in the development of DNA sequencing techniques that enabled the establishment of comprehensive genome sequencing projects. In 1975, he and Alan Coulson published

10062-461: The developing diploid embryo sporophyte within its tissues for at least part of its life, even in the seed plants, where the gametophyte itself is nurtured by its parent sporophyte. Other groups of organisms that were previously studied by botanists include bacteria (now studied in bacteriology ), fungi ( mycology ) – including lichen -forming fungi ( lichenology ), non- chlorophyte algae ( phycology ), and viruses ( virology ). However, attention

10191-448: The development of high-throughput sequencing technologies that parallelize the sequencing process, producing thousands or millions of sequences at once. High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing, as many as 500,000 sequencing-by-synthesis operations may be run in parallel. The Illumina dye sequencing method

10320-463: The earliest was the Padua botanical garden . These gardens facilitated the academic study of plants. Efforts to catalogue and describe their collections were the beginnings of plant taxonomy and led in 1753 to the binomial system of nomenclature of Carl Linnaeus that remains in use to this day for the naming of all biological species. In the 19th and 20th centuries, new techniques were developed for

10449-419: The efforts of early humans to identify – and later cultivate – plants that were edible, poisonous, and possibly medicinal, making it one of the first endeavours of human investigation. Medieval physic gardens , often attached to monasteries , contained plants possibly having medicinal benefit. They were forerunners of the first botanical gardens attached to universities , founded from the 1540s onwards. One of

10578-623: The evolutionary origin of photosynthesis , or estimation of the contribution of horizontal gene transfer to the genomes that have been analyzed. Genomics has provided applications in many fields, including medicine , biotechnology , anthropology and other social sciences . Next-generation genomic technologies allow clinicians and biomedical researchers to drastically increase the amount of genomic data collected on large study populations. When combined with new informatics approaches that integrate many kinds of data with genomic data in disease research, this allows researchers to better understand

10707-453: The extensive earlier work of Alphonse de Candolle , Nikolai Vavilov (1887–1943) produced accounts of the biogeography , centres of origin , and evolutionary history of economic plants. Particularly since the mid-1960s there have been advances in understanding of the physics of plant physiological processes such as transpiration (the transport of water within plant tissues), the temperature dependence of rates of water evaporation from

10836-422: The first eukaryotic chromosome , chromosome III of brewer's yeast Saccharomyces cerevisiae (315 kb) was sequenced. The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8 Mb [megabase]) in 1995. The following year a consortium of researchers from laboratories across North America , Europe , and Japan announced the completion of the first complete genome sequence of

10965-473: The following quarter-century of research. In the same year Walter Gilbert and Allan Maxam of Harvard University independently developed the Maxam-Gilbert method (also known as the chemical method ) of DNA sequencing, involving the preferential cleavage of DNA at known bases, a less efficient method. For their groundbreaking work in the sequencing of nucleic acids, Gilbert and Sanger shared half

11094-575: The fossil record. It is widely regarded as a marker for the start of land plant evolution during the Ordovician period. The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the Ordovician and Silurian periods. Many monocots like maize and the pineapple and some dicots like the Asteraceae have since independently evolved pathways like Crassulacean acid metabolism and

11223-430: The function of DNA at the levels of genes, RNA transcripts, and protein products. 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 "gene-by-gene" approach. A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created

11352-451: The functional relationships between plants and their habitats  – the environments where they complete their life cycles . Plant ecologists study the composition of local and regional floras , their biodiversity , genetic diversity and fitness , the adaptation of plants to their environment, and their competitive or mutualistic interactions with other species. Some ecologists even rely on empirical data from indigenous people that

11481-480: The genetic bases of drug response and disease. Early efforts to apply the genome to medicine included those by a Stanford team led by Euan Ashley who developed the first tools for the medical interpretation of a human genome. The Genomes2People research program at Brigham and Women’s Hospital , Broad Institute and Harvard Medical School was established in 2012 to conduct empirical research in translating genomics into health. Brigham and Women's Hospital opened

11610-607: The genome of progeny. This beneficial effect is also known as hybrid vigor or heterosis. Once outcrossing is established, subsequent switching to inbreeding becomes disadvantageous since it allows expression of the previously masked deleterious recessive mutations, commonly referred to as inbreeding depression. Genomics The field also includes studies of intragenomic (within the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour), and other interactions between loci and alleles within

11739-571: The genome. From the Greek ΓΕΝ gen , "gene" (gamma, epsilon, nu, epsilon) meaning "become, create, creation, birth", and subsequent variants: genealogy, genesis, genetics, genic, genomere, genotype, genus etc. While the word genome (from the German Genom , attributed to Hans Winkler ) was in use in English as early as 1926, the term genomics was coined by Tom Roderick, a geneticist at

11868-444: The global carbon and water cycles and plant roots bind and stabilise soils, preventing soil erosion . Plants are crucial to the future of human society as they provide food, oxygen, biochemicals , and products for people, as well as creating and preserving soil. Historically, all living things were classified as either animals or plants and botany covered the study of all organisms not considered animals. Botanists examine both

11997-425: The growth in the use of the term has led some scientists ( Jonathan Eisen , among others ) to claim that it has been oversold, it reflects the change in orientation towards the quantitative analysis of complete or near-complete assortment of all the constituents of a system. In the study of symbioses , for example, researchers which were once limited to the study of a single gene product can now simultaneously compare

12126-621: The important botanical questions of the 21st century are the role of plants as primary producers in the global cycling of life's basic ingredients: energy, carbon, oxygen, nitrogen and water, and ways that our plant stewardship can help address the global environmental issues of resource management , conservation , human food security , biologically invasive organisms , carbon sequestration , climate change , and sustainability . Virtually all staple foods come either directly from primary production by plants, or indirectly from animals that eat them. Plants and other photosynthetic organisms are at

12255-438: The information gathered by genomic sequencing in order to better evaluate genetic factors key to species conservation, such as the genetic diversity of a population or whether an individual is heterozygous for a recessive inherited genetic disorder. By using genomic data to evaluate the effects of evolutionary processes and to detect patterns in variation throughout a given population, conservationists can formulate plans to aid

12384-467: The instrument depends only on the A/D conversion rate of the camera. The camera takes images of the fluorescently labeled nucleotides, then the dye along with the terminal 3' blocker is chemically removed from the DNA, allowing the next cycle. An alternative approach, ion semiconductor sequencing, is based on standard DNA replication chemistry. This technology measures the release of a hydrogen ion each time

12513-478: The internal functions and processes within plant organelles , cells, tissues, whole plants, plant populations and plant communities. At each of these levels, a botanist may be concerned with the classification ( taxonomy ), phylogeny and evolution , structure ( anatomy and morphology ), or function ( physiology ) of plant life. The strictest definition of "plant" includes only the "land plants" or embryophytes , which include seed plants (gymnosperms, including

12642-403: The leaf shapes and sizes of ancient land plants . Ozone depletion can expose plants to higher levels of ultraviolet radiation-B (UV-B), resulting in lower growth rates. Moreover, information from studies of community ecology , plant systematics , and taxonomy is essential to understanding vegetation change , habitat destruction and species extinction . Inheritance in plants follows

12771-576: The leaf surface and the molecular diffusion of water vapour and carbon dioxide through stomatal apertures. These developments, coupled with new methods for measuring the size of stomatal apertures, and the rate of photosynthesis have enabled precise description of the rates of gas exchange between plants and the atmosphere. Innovations in statistical analysis by Ronald Fisher , Frank Yates and others at Rothamsted Experimental Station facilitated rational experimental design and data analysis in botanical research. The discovery and identification of

12900-576: The maintenance of biodiversity . Botany originated as herbalism , the study and use of plants for their possible medicinal properties . The early recorded history of botany includes many ancient writings and plant classifications. Examples of early botanical works have been found in ancient texts from India dating back to before 1100 BCE, Ancient Egypt , in archaic Avestan writings, and in works from China purportedly from before 221 BCE. Modern botany traces its roots back to Ancient Greece specifically to Theophrastus ( c.  371 –287 BCE),

13029-493: The major groups of organisms that carry out photosynthesis , a process that uses the energy of sunlight to convert water and carbon dioxide into sugars that can be used both as a source of chemical energy and of organic molecules that are used in the structural components of cells. As a by-product of photosynthesis, plants release oxygen into the atmosphere, a gas that is required by nearly all living things to carry out cellular respiration. In addition, they are influential in

13158-474: The mechanisms and control of gene expression during differentiation of plant cells and tissues . Botanical research has diverse applications in providing staple foods , materials such as timber , oil , rubber, fibre and drugs, in modern horticulture , agriculture and forestry , plant propagation , breeding and genetic modification , in the synthesis of chemicals and raw materials for construction and energy production, in environmental management , and

13287-596: The number of their male sexual organs. The 24th group, Cryptogamia , included all plants with concealed reproductive parts, mosses , liverworts , ferns , algae and fungi . Botany was originally a hobby for upper-class women. These women would collect and paint flowers and plants from around the world with scientific accuracy. The paintings were used to record many species that could not be transported or maintained in other environments. Marianne North illustrated over 900 species in extreme detail with watercolor and oil paintings. Her work and many other women's botany work

13416-447: The other hand with medicine and pharmacology, giving rise to fields such as agronomy , horticultural botany, phytopathology and phytopharmacology . The study of plants is vital because they underpin almost all animal life on Earth by generating a large proportion of the oxygen and food that provide humans and other organisms with aerobic respiration with the chemical energy they need to exist. Plants, algae and cyanobacteria are

13545-404: The outcome of prehistoric selection over thousands of years from among wild ancestral plants with the most desirable characteristics. Botanists study how plants produce food and how to increase yields, for example through plant breeding , making their work important to humanity's ability to feed the world and provide food security for future generations. Botanists also study weeds, which are

13674-791: The pain killer aspirin is the acetyl ester of salicylic acid , originally isolated from the bark of willow trees, and a wide range of opiate painkillers like heroin are obtained by chemical modification of morphine obtained from the opium poppy . Popular stimulants come from plants, such as caffeine from coffee, tea and chocolate, and nicotine from tobacco. Most alcoholic beverages come from fermentation of carbohydrate -rich plant products such as barley (beer), rice ( sake ) and grapes (wine). Native Americans have used various plants as ways of treating illness or disease for thousands of years. This knowledge Native Americans have on plants has been recorded by enthnobotanists and then in turn has been used by pharmaceutical companies as

13803-490: The plants with a highly fermentable sugar or oil content that are used as sources of biofuels , important alternatives to fossil fuels , such as biodiesel . Sweetgrass was used by Native Americans to ward off bugs like mosquitoes . These bug repelling properties of sweetgrass were later found by the American Chemical Society in the molecules phytol and coumarin . Plant ecology is the science of

13932-486: The pollen either fails to reach the stigma or fails to germinate and produce male gametes . This is one of several methods used by plants to promote outcrossing . In many land plants the male and female gametes are produced by separate individuals. These species are said to be dioecious when referring to vascular plant sporophytes and dioicous when referring to bryophyte gametophytes . Charles Darwin in his 1878 book The Effects of Cross and Self-Fertilization in

14061-442: The polymer cutin which is found in the plant cuticle that protects land plants from drying out. Plants synthesise a number of unique polymers like the polysaccharide molecules cellulose , pectin and xyloglucan from which the land plant cell wall is constructed. Vascular land plants make lignin , a polymer used to strengthen the secondary cell walls of xylem tracheids and vessels to keep them from collapsing when

14190-415: The possibility for the field of functional genomics , mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics . Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome . This genome-based approach allows for a high-throughput method of structure determination by

14319-556: The practical value of earlier "physic gardens", often associated with monasteries, in which plants were cultivated for suspected medicinal uses. They supported the growth of botany as an academic subject. Lectures were given about the plants grown in the gardens. Botanical gardens came much later to northern Europe; the first in England was the University of Oxford Botanic Garden in 1621. German physician Leonhart Fuchs (1501–1566)

14448-433: The previously 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. Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology . Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced

14577-544: The regional flora of the East Frisian Islands , Flora der Ostfriesischen Inseln , and of Bremen / Oldenburg , Flora von Bremen und Oldenburg . He also published a comprehensive monograph on the botanical family Juncaceae , titled Monographia Juncacearum . This article about a German botanist is a stub . You can help Misplaced Pages by expanding it . Botanist Botany , also called plant science (or plant sciences ), plant biology or phytology ,

14706-461: The rise of the related molecular-scale biological approaches of molecular biology , genomics , proteomics and metabolomics , the relationship between the plant genome and most aspects of the biochemistry, physiology, morphology and behaviour of plants can be subjected to detailed experimental analysis. The concept originally stated by Gottlieb Haberlandt in 1902 that all plant cells are totipotent and can be grown in vitro ultimately enabled

14835-660: The same annotation pipeline (also see below ). Traditionally, the basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on homologues. More recently, additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl ) rely on both curated data sources as well as

14964-680: The same fundamental principles of genetics as in other multicellular organisms. Gregor Mendel discovered the genetic laws of inheritance by studying inherited traits such as shape in Pisum sativum ( peas ). What Mendel learned from studying plants has had far-reaching benefits outside of botany. Similarly, " jumping genes " were discovered by Barbara McClintock while she was studying maize. Nevertheless, there are some distinctive genetic differences between plants and other organisms. Species boundaries in plants may be weaker than in animals, and cross species hybrids are often possible. A familiar example

15093-473: The structure of DNA in 1953 and Fred Sanger 's publication of the Amino acid sequence of insulin in 1955, nucleic acid sequencing became a major target of early molecular biologists . In 1964, Robert W. Holley and colleagues published the first nucleic acid sequence ever determined, the ribonucleotide sequence of alanine transfer RNA . Extending this work, Marshall Nirenberg and Philip Leder revealed

15222-603: The study of fungi and algae by mycologists and phycologists respectively, with the study of these three groups of organisms remaining within the sphere of interest of the International Botanical Congress . Nowadays, botanists (in the strict sense) study approximately 410,000 species of land plants , including some 391,000 species of vascular plants (of which approximately 369,000 are flowering plants ) and approximately 20,000 bryophytes . Botany originated in prehistory as herbalism with

15351-450: The study of plants, including methods of optical microscopy and live cell imaging , electron microscopy , analysis of chromosome number , plant chemistry and the structure and function of enzymes and other proteins . In the last two decades of the 20th century, botanists exploited the techniques of molecular genetic analysis , including genomics and proteomics and DNA sequences to classify plants more accurately. Modern botany

15480-471: The study of plants. In 1665, using an early microscope, Polymath Robert Hooke discovered cells (a term he coined) in cork , and a short time later in living plant tissue. During the 18th century, systems of plant identification were developed comparable to dichotomous keys , where unidentified plants are placed into taxonomic groups (e.g. family, genus and species) by making a series of choices between pairs of characters . The choice and sequence of

15609-405: The target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing is a random sampling process, requiring over-sampling to ensure a given nucleotide is represented in the reconstructed sequence; the average number of reads by which a genome

15738-507: The total complement of several types of biological molecules. After an organism has been selected, genome projects involve three components: the sequencing of DNA, the assembly of that sequence to create a representation of the original chromosome, and the annotation and analysis of that representation. Historically, sequencing was done in sequencing centers , centralized facilities (ranging from large independent institutions such as Joint Genome Institute which sequence dozens of terabases

15867-480: The triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in their experiments. In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent ( Ghent , Belgium ) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein. Fiers' group expanded on their MS2 coat protein work, determining

15996-526: The use of genetic engineering experimentally to knock out a gene or genes responsible for a specific trait, or to add genes such as GFP that report when a gene of interest is being expressed. These technologies enable the biotechnological use of whole plants or plant cell cultures grown in bioreactors to synthesise pesticides , antibiotics or other pharmaceuticals , as well as the practical application of genetically modified crops designed for traits such as improved yield. Modern morphology recognises

16125-485: The word plant (e.g. plant taxonomy, plant ecology, plant anatomy, plant morphology, plant systematics, plant ecology), or prefixing or substituting the prefix phyto- (e.g. phytochemistry , phytogeography ). The study of fossil plants is palaeobotany . Other fields are denoted by adding or substituting the word botany (e.g. systematic botany ). Phytosociology is a subfield of plant ecology that classifies and studies communities of plants. The intersection of fields from

16254-507: Was a bacteriophage . However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that

16383-492: Was a big improvement, but was still very laborious. Nevertheless, in 1977 his group was able to sequence most of the 5,386 nucleotides of the single-stranded bacteriophage φX174 , completing the first fully sequenced DNA-based genome. The refinement of the Plus and Minus method resulted in the chain-termination, or Sanger method (see below ), which formed the basis of the techniques of DNA sequencing, genome mapping, data storage, and bioinformatic analysis most widely used in

16512-399: Was one of "the three German fathers of botany", along with theologian Otto Brunfels (1489–1534) and physician Hieronymus Bock (1498–1554) (also called Hieronymus Tragus). Fuchs and Brunfels broke away from the tradition of copying earlier works to make original observations of their own. Bock created his own system of plant classification. Physician Valerius Cordus (1515–1544) authored

16641-412: Was the beginning of popularizing botany to a wider audience. Increasing knowledge of plant anatomy , morphology and life cycles led to the realisation that there were more natural affinities between plants than the artificial sexual system of Linnaeus. Adanson (1763), de Jussieu (1789), and Candolle (1819) all proposed various alternative natural systems of classification that grouped plants using

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