The coding region of a gene, also known as the coding sequence(CDS), is the portion of a gene's DNA or RNA that codes for protein.
Studying the length, composition, regulation, splicing, structures, and
functions of coding regions compared to non-coding regions over
different species and time periods can provide a significant amount of
important information regarding gene organization and evolution of prokaryotes and eukaryotes. This can further assist in mapping the human genome and developing gene therapy.
Definition
Although this term is also sometimes used interchangeably with exon, it is not the exact same thing: the exon is composed of the coding region as well as the 3' and 5' untranslated regions of the RNA, and so therefore, an exon would be partially made up of coding regions. The 3' and 5' untranslated regions of the RNA, which do not code for protein, are termed non-coding regions and are not discussed on this page.
There is often confusion between coding regions and exomes and there is a clear distinction between these terms. While the exome
refers to all exons within a genome, the coding region refers to a
singular section of the DNA or RNA which specifically codes for a
certain kind of protein.
History
In 1978, Walter Gilbert published "Why Genes in Pieces" which first began to explore the idea that the gene is a mosaic—that each full nucleic acid
strand is not coded continuously but is interrupted by "silent"
non-coding regions. This was the first indication that there needed to
be a distinction between the parts of the genome that code for protein,
now called coding regions, and those that do not.
Composition
Point mutation types: transitions (blue) are elevated compared to transversions (red) in GC-rich coding regions.
The evidence suggests that there is a general interdependence between base composition patterns and coding region availability. The coding region is thought to contain a higher GC-content
than non-coding regions. There is further research that discovered that
the longer the coding strand, the higher the GC-content. Short coding
strands are comparatively still GC-poor, similar to the low GC-content
of the base composition translational stop codons like TAG, TAA, and TGA.
GC-rich areas are also where the ratio point mutation type is altered slightly: there are more transitions, which are changes from purine to purine or pyrimidine to pyrimidine, compared to transversions,
which are changes from purine to pyrimidine or pyrimidine to purine.
The transitions are less likely to change the encoded amino acid and
remain a silent mutation (especially if they occur in the third nucleotide of a codon) which is usually beneficial to the organism during translation and protein formation.
This indicates that essential coding regions (gene-rich) are higher in GC-content and more stable and resistant to mutation compared to accessory and non-essential regions (gene-poor). However, it is still unclear whether this came about through neutral and random mutation or through a pattern of selection.
There is also debate on whether the methods used, such as gene windows,
to ascertain the relationship between GC-content and coding region are
accurate and unbiased.
Structure and function
Transcription:
RNA Polymerase (RNAP) uses a template DNA strand and begins coding at
the promoter sequence (green) and ends at the terminator sequence (red)
in order to encompass the entire coding region into the pre-mRNA (teal).
The pre-mRNA is polymerised 5' to 3' and the template DNA read 3' to 5'
An
electron-micrograph of DNA strands decorated by hundreds of RNAP
molecules too small to be resolved. Each RNAP is transcribing an RNA
strand, which can be seen branching off from the DNA. "Begin" indicates
the 3' end of the DNA, where RNAP initiates transcription; "End"
indicates the 5' end, where the longer RNA molecules are completely
transcribed.
In DNA, the coding region is flanked by the promoter sequence on the 5' end of the template strand and the termination sequence on the 3' end. During transcription, the RNA Polymerase (RNAP) binds to the promoter sequence and moves along the template strand to the coding region. RNAP then adds RNA nucleotides complementary to the coding region in order to form the mRNA, substituting uracil in place of thymine. This continues until the RNAP reaches the termination sequence.
After transcription and maturation, the mature mRNA formed encompasses multiple parts important for its eventual translation into protein. The coding region in an mRNA is flanked by the 5' untranslated region (5'-UTR) and 3' untranslated region (3'-UTR), the 5' cap, and Poly-A tail. During translation, the ribosome facilitates the attachment of the tRNAs to the coding region, 3 nucleotides at a time (codons). The tRNAs transfer their associated amino acids to the growing polypeptide chain, eventually forming the protein defined in the initial DNA coding region.
The coding region (teal) is flanked by untranslated regions, the 5' cap, and the poly(A) tail which together form the mature mRNA.
Regulation
The coding region can be modified in order to regulate gene expression.
Alkylation is one form of regulation of the coding region.
The gene that would have been transcribed can be silenced by targeting a
specific sequence. The bases in this sequence would be blocked using alkyl groups, which create the silencing effect.
While the regulation of gene expression manages the abundance of RNA or protein made in a cell, the regulation of these mechanisms can be controlled by a regulatory sequence found before the open reading frame begins in a strand of DNA. The regulatory sequence will then determine the location and time that expression will occur for a protein coding region.
RNA splicing
ultimately determines what part of the sequence becomes translated and
expressed, and this process involves cutting out introns and putting
together exons. Where the RNA spliceosome cuts, however, is guided by the recognition of splice sites, in particular the 5' splicing site, which is one of the substrates for the first step in splicing. The coding regions are within the exons, which become covalently joined together to form the mature messenger RNA.
Mutations
Mutations
in the coding region can have very diverse effects on the phenotype of
the organism. While some mutations in this region of DNA/RNA can result
in advantageous changes, others can be harmful and sometimes even lethal
to an organism's survival. In contrast, changes in the coding region
may not always result in detectable changes in phenotype.
Mutation types
Examples of the various forms of point mutations
that may exist within coding regions. Such alterations may or may not
have phenotypic changes, depending on whether or not they code for
different amino acids during translation.
There are various forms of mutations that can occur in coding regions. One form is silent mutations, in which a change in nucleotides does not result in any change in amino acid after transcription and translation. There also exist nonsense mutations, where base alterations in the coding region code for a premature stop codon, producing a shorter final protein. Point mutations, or single base pair changes in the coding region, that code for different amino acids during translation, are called missense mutations. Other types of mutations include frameshift mutations such as insertions or deletions.
Formation
Some forms of mutations are hereditary (germline mutations), or passed on from a parent to its offspring. Such mutated coding regions are present in all cells within the organism. Other forms of mutations are acquired (somatic mutations) during an organisms lifetime, and may not be constant cell-to-cell. These changes can be caused by mutagens, carcinogens, or other environmental agents (ex. UV). Acquired mutations can also be a result of copy-errors during DNA replication and are not passed down to offspring. Changes in the coding region can also be de novo (new); such changes are thought to occur shortly after fertilization, resulting in a mutation present in the offspring's DNA while being absent in both the sperm and egg cells.
Prevention
There
exist multiple transcription and translation mechanisms to prevent
lethality due to deleterious mutations in the coding region. Such
measures include proofreading by some DNA Polymerases during replication, mismatch repair following replication, and the 'Wobble Hypothesis' which describes the degeneracy of the third base within an mRNA codon.
Constrained coding regions (CCRs)
While
it is well known that the genome of one individual can have extensive
differences when compared to the genome of another, recent research has
found that some coding regions are highly constrained, or resistant to
mutation, between individuals of the same species. This is similar to
the concept of interspecies constraint in conserved sequences.
Researchers termed these highly constrained sequences constrained
coding regions (CCRs), and have also discovered that such regions may be
involved in high purifying selection.
On average, there is approximately 1 protein-altering mutation every 7
coding bases, but some CCRs can have over 100 bases in sequence with no
observed protein-altering mutations, some without even synonymous
mutations. These patterns of constraint between genomes may provide clues to the sources of rare developmental diseases or potentially even embryonic lethality. Clinically validated variants and de novo mutations in CCRs have been previously linked to disorders such as infantile epileptic encephalopathy, developmental delay and severe heart disease.
Coding sequence detection
While identification of open reading frames
within a DNA sequence is straightforward, identifying coding sequences
is not, because the cell translates only a subset of all open reading
frames to proteins.
Currently CDS prediction uses sampling and sequencing of mRNA from
cells, although there is still the problem of determining which parts of
a given mRNA are actually translated to protein. CDS prediction is a
subset of gene prediction,
the latter also including prediction of DNA sequences that code not
only for protein but also for other functional elements such as RNA
genes and regulatory sequences.
In both prokaryotes and eukaryotes, gene overlapping
occurs relatively often in both DNA and RNA viruses as an evolutionary
advantage to reduce genome size while retaining the ability to produce
various proteins from the available coding regions. For both DNA and RNA, pairwise alignments can detect overlapping coding regions, including short open reading frames in viruses, but would require a known coding strand to compare the potential overlapping coding strand with.
An alternative method using single genome sequences would not require
multiple genome sequences to execute comparisons but would require at
least 50 nucleotides overlapping in order to be sensitive.
Flowers or clusters of flowers produced by twelve species of Angiosperms from different families.
Selection of differently constructed flowers at different stages of vascular plant development
A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants (plants of the division Angiospermae). The biological function of a flower is to facilitate reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate outcrossing (fusion of sperm and eggs from different individuals in a population) resulting from cross-pollination or allow selfing (fusion of sperm and egg from the same flower) when self-pollination occurs.
There are two types of pollination: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma
of the same flower, or another flower on the same plant.
Cross-pollination is when pollen is transferred from the anther of one
flower to the stigma of another flower on a different individual of the
same species. Self-pollination happens in flowers where the stamen and carpel
mature at the same time, and are positioned so that the pollen can land
on the flower's stigma. This pollination does not require an investment
from the plant to provide nectar and pollen as food for pollinators.
Many flowers have evolved to be attractive to animals, so as to cause them to be vectors for the transfer of pollen. After fertilization, the ovary of the flower develops into fruit containing seeds.
In addition to facilitating the reproduction of flowering plants,
flowers have long been admired and used by humans to bring beauty to
the environment, and also as objects of romance, ritual, esotericism, witchcraft, religion, holistic medicine, and as a source of food.
Etymology
Flower is from the Middle Englishflour, which referred to both the ground grain and the reproductive structure in plants, before splitting off in the 17th century. It comes originally from the Latin name of the Italian goddess of flowers, Flora. The early word for flower in English was blossom, though it now refers to flowers only of fruit trees.
The morphology of a flower, or its form and structure, can be considered in two parts: the vegetative part, consisting of non-reproductive structures such as petals;
and the reproductive or sexual parts. A stereotypical flower is made up
of four kinds of structures attached to the tip of a short stalk or
axis, called a receptacle. Each of these parts or floral organs is arranged in a spiral called a whorl. The four main whorls (starting from the base of the flower or lowest node and working upwards) are the calyx, corolla, androecium, and gynoecium. Together the calyx and corolla make up the non-reproductive part of the flower called the perianth, and in some cases may not be differentiated. If this is the case, then they are described as tepals.
The sepals, collectively called the calyx, are modified leaves that occur on the outermost whorl of the flower. They are leaf-like, in that they have a broad base, stomata, stipules, and chlorophyll. Sepals are often waxy and tough, and grow quickly to protect the flower as it develops. They may be deciduous, but will more commonly grow on to assist in fruit dispersal. If the calyx is fused together it is called gamosepalous.
Corolla
The petals,
together the corolla, are almost or completely fiberless leaf-like
structures that form the innermost whorl of the perianth. They are often
delicate and thin, and are usually coloured, shaped, or scented to
encourage pollination.
Although similar to leaves in shape, they are more comparable to
stamens in that they form almost simultaneously with one another, but
their subsequent growth is delayed. If the corolla is fused together it
is called sympetalous.
Reproductive parts of Easter Lily (Lilium longiflorum). 1. Stigma, 2. Style, 3. Stamens, 4. Filament, 5. Petal
Androecium
The androecium,
or stamens, is the whorl of pollen producing male parts. Stamens
consist typically of an anther, made up of four pollen sacs arranged in
two thecae, connected to a filament, or stalk. The anther contains microsporocytes which become pollen, the male gametophyte, after undergoing meiosis.
Although they exhibit the widest variation among floral organs, the
androecium is usually confined just to one whorl and to two whorls only
in rare cases. Stamens range in number, size, shape, orientation, and in
their point of connection to the flower.
Gynoecium
The gynoecium, or the carpels, is the female part of the flower found on the innermost whorl. Each carpel consists of a stigma, which receives pollen, a style, which acts as a stalk, and an ovary,
which contains the ovules. Carpels may occur in one to several whorls,
and when fused together are often described as a pistil. Inside the
ovary, the ovules are suspended off of pieces of tissue called placenta.
Variation
Although this arrangement is considered "typical", plant species show a wide variation in floral structure.
The four main parts of a flower are generally defined by their
positions on the receptacle and not by their function. Many flowers lack
some parts or parts may be modified into other functions or look like
what is typically another part. In some families, like Ranunculaceae,
the petals are greatly reduced and in many species the sepals are
colorful and petal-like. Other flowers have modified stamens that are
petal-like; the double flowers of Peonies and Roses are mostly petaloid stamens.
Many flowers have a symmetry. When the perianth is bisected through the central axis from any point and symmetrical halves are produced, the flower is said to be actinomorphic or regular. This is an example of radial symmetry. When flowers are bisected and produce only one line that produces symmetrical halves, the flower is said to be irregular or zygomorphic. If, in rare cases, they have no symmetry at all they are called asymmetric.
Flowers may be directly attached to the plant at their base (sessile—the supporting stalk or stem is highly reduced or absent). The stem or stalk subtending a flower, or an inflorescence of flowers, is called a peduncle. If a peduncle supports more than one flower, the stems connecting each flower to the main axis are called pedicels. The apex of a flowering stem forms a terminal swelling which is called the torus or receptacle.
In the majority of species individual flowers have both pistils and stamens. These flowers are described by botanists as being perfect, bisexual, or hermaphrodite.
However, in some species of plants the flowers are imperfect or
unisexual: having only either male (stamens) or female (pistil) parts.
In the latter case, if an individual plant is either female or male the
species is regarded as dioecious. However, where unisexual male and female flowers appear on the same plant, the species is called monoecious. Many flowers have nectaries, which are glands that produce a sugary fluid used to attract pollinators. They are not considered as an organ on their own.
The calla lily is not a single flower. It is actually an inflorescence of tiny flowers pressed together on a central stalk that is surrounded by a large petal-like bract.
In those species that have more than one flower on an axis, the collective cluster of flowers is called an inflorescence.
Some inflorescences are composed of many small flowers arranged in a
formation that resembles a single flower. The common example of this is
most members of the very large composite (Asteraceae) group. A single daisy or sunflower, for example, is not a flower but a flower head—an inflorescence composed of numerous flowers (or florets). An inflorescence may include specialized stems and modified leaves known as bracts.
A floral formula is a way to represent the structure of a
flower using specific letters, numbers and symbols, presenting
substantial information about the flower in a compact form. It can
represent a taxon,
usually giving ranges of the numbers of different organs, or particular
species. Floral formulae have been developed in the early 19th century
and their use has declined since. Prenner et al. (2010) devised an extension of the existing model to broaden the descriptive capability of the formula. The format of floral formulae differs in different parts of the world, yet they convey the same information.
The structure of a flower can also be expressed by the means of floral diagrams.
The use of schematic diagrams can replace long descriptions or
complicated drawings as a tool for understanding both floral structure
and evolution. Such diagrams may show important features of flowers,
including the relative positions of the various organs, including the
presence of fusion and symmetry, as well as structural details.
Development
A flower develops on a modified shoot or axis from a determinate apical meristem (determinate
meaning the axis grows to a set size). It has compressed internodes,
bearing structures that in classical plant morphology are interpreted as
highly modified leaves. Detailed developmental studies, however, have shown that stamens are often initiated more or less like modified stems (caulomes) that in some cases may even resemble branchlets.
Taking into account the whole diversity in the development of the
androecium of flowering plants, we find a continuum between modified
leaves (phyllomes), modified stems (caulomes), and modified branchlets
(shoots).
Transition
The transition to flowering is one of the major phase changes that a
plant makes during its life cycle. The transition must take place at a
time that is favorable for fertilization and the formation of seeds, hence ensuring maximal reproductive
success. To meet these needs a plant is able to interpret important
endogenous and environmental cues such as changes in levels of plant hormones and seasonable temperature and photoperiod changes. Many perennial and most biennial plants require vernalization to flower. The molecular interpretation of these signals is through the transmission of a complex signal known as florigen, which involves a variety of genes,
including Constans, Flowering Locus C and Flowering Locus T. Florigen
is produced in the leaves in reproductively favorable conditions and
acts in buds and growing tips to induce a number of different physiological and morphological changes.
The ABC model of flower development
The
first step of the transition is the transformation of the vegetative
stem primordia into floral primordia. This occurs as biochemical changes
take place to change cellular differentiation of leaf, bud and stem
tissues into tissue that will grow into the reproductive organs. Growth
of the central part of the stem tip stops or flattens out and the sides
develop protuberances in a whorled or spiral fashion around the outside
of the stem end. These protuberances develop into the sepals, petals,
stamens, and carpels.
Once this process begins, in most plants, it cannot be reversed and the
stems develop flowers, even if the initial start of the flower
formation event was dependent of some environmental cue.
The ABC model is a simple model that describes the genes
responsible for the development of flowers. Three gene activities
interact in a combinatorial manner to determine the developmental
identities of the primordia organ within the floral apical meristem.
These gene functions are called A, B, and C. A genes are expressed in
only outer and lower most section of the apical meristem, which becomes a
whorl of sepals. In the second whorl both A and B genes are expressed,
leading to the formation of petals. In the third whorl, B and C genes
interact to form stamens and in the center of the flower C genes alone
give rise to carpels. The model is based upon studies of aberrant
flowers and mutations in Arabidopsis thaliana and the snapdragon, Antirrhinum majus.
For example, when there is a loss of B gene function, mutant flowers
are produced with sepals in the first whorl as usual, but also in the
second whorl instead of the normal petal formation. In the third whorl
the lack of B function but presence of C function mimics the fourth
whorl, leading to the formation of carpels also in the third whorl.
The principal purpose of a flower is the reproduction of the individual and the species. All flowering plants are heterosporous, that is, every individual plant produces two types of spores. Microspores are produced by meiosis
inside anthers and megaspores are produced inside ovules that are
within an ovary. Anthers typically consist of four microsporangia and an
ovule is an integumented megasporangium. Both types of spores develop
into gametophytes
inside sporangia. As with all heterosporous plants, the gametophytes
also develop inside the spores, i. e., they are endosporic.
In the majority of plant species, individual flowers have both
functional carpels and stamens. Botanists describe these flowers as
perfect or bisexual, and the species as hermaphroditic.
In a minority of plant species, their flowers lack one or the other
reproductive organ and are described as imperfect or unisexual. If the
individual plants of a species each have unisexual flowers of both sexes
then the species is monoecious. Alternatively, if each individual plant has only unisexual flowers of the same sex then the species is dioecious.
Grains of pollen sticking to this bee will be transferred to the next flower it visits.
The primary purpose of the flower is reproduction.
Since the flowers are the reproductive organs of the plant, they
mediate the joining of the sperm, contained within pollen, to the ovules
— contained in the ovary. Pollination is the movement of pollen from the anthers to the stigma. Normally pollen is moved from one plant to another, known as cross-pollination, but many plants are able to self-pollinate. Cross-pollination is preferred because it allows for genetic variation, which contributes to the survival of the species. Many flowers are dependent, then, upon external factors for pollination, such as: the wind, water, animals, and especially insects. Larger animals such as birds, bats, and even some pygmy possums, however, can also be employed.
To accomplish this, flowers have specific designs which encourage the
transfer of pollen from one plant to another of the same species. The
period of time during which this process can take place (when the flower
is fully expanded and functional) is called anthesis, hence the study of pollination biology is called anthecology.
Flowering plants usually face evolutionary pressure to optimize the transfer of their pollen, and this is typically reflected in the morphology of the flowers and the behaviour of the plants.
Pollen may be transferred between plants via a number of 'vectors,' or
methods. Around 80% of flowering plants make use of biotic, or living
vectors. Others use abiotic, or non-living, vectors and some plants make
use of multiple vectors, but most are highly specialised.
Though some fit between or outside of these groups, most flowers can be divided between the following two broad groups of pollination methods:
Biotic pollination
Flowers that use biotic vectors attract and use insects, bats, birds, or other animals to transfer pollen from one flower to the next. Often they are specialized
in shape and have an arrangement of the stamens that ensures that
pollen grains are transferred to the bodies of the pollinator when it
lands in search of its attractant (such as nectar, pollen, or a mate).
In pursuing this attractant from many flowers of the same species, the
pollinator transfers pollen to the stigmas—arranged with equally pointed
precision—of all of the flowers it visits.
Many flowers rely on simple proximity between flower parts to ensure
pollination, while others have elaborate designs to ensure pollination
and prevent self-pollination. Flowers use animals including: insects (entomophily), birds (ornithophily), bats (chiropterophily), lizards, and even snails and slugs (malacophilae).
Attraction methods
Ophrys apifera, a bee orchid, which has evolved over many generations to mimic a female bee.
Plants cannot move from one location to another, thus many flowers
have evolved to attract animals to transfer pollen between individuals
in dispersed populations. Most commonly, flowers are insect-pollinated,
known as entomophilous; literally "insect-loving" in Greek. To attract these insects flowers commonly have glands called nectaries on various parts that attract animals looking for nutritious nectar. Birds and bees have color vision, enabling them to seek out "colorful" flowers. Some flowers have patterns, called nectar guides, that show pollinators where to look for nectar; they may be visible only under ultraviolet light, which is visible to bees and some other insects.
Flowers also attract pollinators by scent,
though not all flower scents are appealing to humans; a number of
flowers are pollinated by insects that are attracted to rotten flesh and
have flowers that smell like dead animals. These are often called Carrion flowers, including plants in the genus Rafflesia, and the titan arum.
Flowers pollinated by night visitors, including bats and moths, are
likely to concentrate on scent to attract pollinators and so most such
flowers are white.
Flowers are also specialized in shape and have an arrangement of the stamens
that ensures that pollen grains are transferred to the bodies of the
pollinator when it lands in search of its attractant. Other flowers use
mimicry or pseudocopulation
to attract pollinators. Many orchids for example, produce flowers
resembling female bees or wasps in colour, shape, and scent. Males move
from one flower to the next in search of a mate, pollinating the
flowers.
Many flowers have close relationships with one or a few specific
pollinating organisms. Many flowers, for example, attract only one
specific species of insect, and therefore rely on that insect for
successful reproduction. This close relationship an example of coevolution, as the flower and pollinator have developed together over a long period of time to match each other's needs. This close relationship compounds the negative effects of extinction,
however, since the extinction of either member in such a relationship
would almost certainly mean the extinction of the other member as well.
A Grass flower with its long, thin filaments and large feathery stigma.
The female flower of Enhalus acoroides, which is pollinated through a combination of Hyphydrogamy and Ephydrogamy.
Flowers that use abiotic, or non-living, vectors use the wind or, much less commonly, water, to move pollen from one flower to the next. In wind-dispersed (anemophilous) species, the tiny pollen grains are carried, sometimes many thousands of kilometres, by the wind to other flowers. Common examples include the grasses, birch trees, along with many other species in the order fagales, ragweeds, and many sedges.
They have no need to attract pollinators and therefore tend not to grow
large, showy, or colorful flowers, and do not have nectaries, nor a
noticeable scent. Because of this, plants typically have many thousands
of tiny flowers which have comparatively large, feathery stigmas; to
increase the chance of pollen being received. Whereas the pollen of entomophilous flowers is usually large, sticky, and rich in protein
(to act as a "reward" for pollinators), anemophilous flower pollen is
typically small-grained, very light, smooth, and of little nutritional
value to insects.
In order for the wind to effectively pick up and transport the pollen,
the flowers typically have anthers loosely attached to the end of long
thin filaments, or pollen forms around a catkin which moves in the wind. Rarer forms of this involve individual flowers being moveable by the wind (Pendulous), or even less commonly; the anthers exploding to release the pollen into the wind.
Pollination through water (hydrophily) is a much rarer method, occurring in only around 2% of abiotically pollinated flowers. Common examples of this include Calitriche autumnalis, Vallisneria spiralis and some sea-grasses. One characteristic which most species in this group share is a lack of an exine, or protective layer, around the pollen grain.
Paul Knuth identified two types of hydrophilous pollination in 1906 and
Ernst Schwarzenbach added a third in 1944. Knuth named his two groups Hyphydrogamy and the more common Ephydrogamy. In Hyphydrogamy pollination occurs below the surface of the water and so the pollen grains are typically negatively buoyant.
For marine plants that exhibit this method the stigmas are usually
stiff, while freshwater species have small and feathery stigmas. In Ephydrogamy
pollination occurs on the surface of the water and so the pollen has a
low density to enable floating, though many also use rafts, and are hydrophobic.
Marine flowers have floating thread-like stigmas and may have
adaptations for the tide, while freshwater species create indentations
in the water.
The third category, set out by Schwarzenbach, is those flowers which
transport pollen above the water through conveyance. This ranges from
floating plants, (Lemnoideae), to staminate flowers (Vallisneria).
Most species in this group have dry, spherical pollen which sometimes
forms into larger masses, and female flowers which form depressions in
the water; the method of transport varies.
Mechanisms
Flowers
can be pollinated by two mechanisms; cross-pollination and
self-pollination. No mechanism is indisputably better than the other as
they each have their advantages and disadvantages. Plants use one or
both of these mechanisms depending on their habitat and ecological niche.
Cross-pollination
Cross-pollination
is the pollination of the carpel by pollen from a different plant of
the same species. Because the genetic make-up of the sperm contained
within the pollen from the other plant is different, their combination
will result in a new, genetically distinct, plant, through the process
of sexual reproduction. Since each new plant is genetically distinct, the different plants show variation in their physiological and structural adaptations and so the population
as a whole is better prepared for an adverse occurrence in the
environment. Cross-pollination, therefore, increases the survival of the
species and is usually preferred by flowers for this reason.
Self-pollination
Clianthus puniceus, the Kaka Beak.
Self-pollination is the pollination of the carpel of a flower by
pollen from either the same flower or another flower on the same plant, leading to the creation of a genetic clone through asexual reproduction.
This increases the reliability of producing seeds, the rate at which
they can be produced, and lowers the amount energy needed. But, most importantly, it limits genetic variation.
The extreme case of self-fertilization, when the ovule is
fertilized by pollen from the same flower or plant, occurs in flowers
that always self-fertilize, such as many dandelions.
Some flowers are self-pollinated and have flowers that never open or
are self-pollinated before the flowers open; these flowers are called cleistogamous; many species in the genus Viola exhibit this, for example.
Conversely, many species of plants have ways of preventing
self-pollination and hence, self-fertilization. Unisexual male and
female flowers on the same plant may not appear or mature at the same
time, or pollen from the same plant may be incapable of fertilizing its
ovules. The latter flower types, which have chemical barriers to their
own pollen, are referred to as self-incompatible.In Clianthus puniceus, (pictured), self-pollination is used strategically as an "insurance policy." When a pollinator, in this case a bird, visits C. puniceus
it rubs off the stigmatic covering and allows for pollen from the bird
to enter the stigma. If no pollinators visit, however, then the
stigmatic covering falls off naturally to allow for the flower's own
anthers to pollinate the flower through self-pollination.
Pollen is a large contributor to asthma and other respiratory allergies
which combined affect between 10 and 50% of people worldwide. This
number appears to be growing, as the temperature increases due to climate change mean that plants are producing more pollen,
which is also more allergenic. Pollen is difficult to avoid, however,
because of its small size and prevalence in the natural environment.
Most of the pollen which causes allergies is that produced by
wind-dispersed pollinators such as the grasses, birch trees, oak trees, and ragweeds; the allergens in pollen are proteins which are thought to be necessary in the process of pollination.
A floral diagram, with the pollen tube labelled PG
Fertilization, also called Synagmy, occurs following pollination, which is the movement of pollen from the stamen to the carpel. It encompasses both plasmogamy, the fusion of the protoplasts, and karyogamy, the fusion of the nuclei. When pollen lands on the stigma of the flower it begins creating a pollen tube
which runs down through the style and into the ovary. After penetrating
the centre-most part of the ovary it enters the egg apparatus and into
one synergid.
At this point the end of the pollen tube bursts and releases the two
sperm cells, one of which makes its way to an egg, while also losing its
cell membrane and much of its protoplasm. The sperm's nucleus then fuses with the egg's nucleus, resulting in the formation of a zygote, a diploid (two copies of each chromosome) cell.
Whereas in fertilization only plasmogamy, or the fusion of the
whole sex cells, results, in Angiosperms (flowering plants) a process
known as double fertilization, which involves both karyogamy and
plasmogamy, occurs. In double fertilization the second sperm cell
subsequently also enters the synergid and fuses with the two polar
nuclei of the central cell. Since all three nuclei are haploid, they result in a large endosperm nucleus which is triploid.
The fruit of a peach with the seed or stone inside.
Following the formation of zygote it begins to grow through nuclear and cellular divisions, called mitosis, eventually becoming a small group of cells. One section of it becomes the embryo, while the other becomes the suspensor; a structure which forces the embryo into the endosperm and is later undetectable. Two small primordia also form at this time, that later become the cotyledon, which is used as an energy store. Plants which grow out one of these primordia are called monocotyledons, while those that grow out two are dicotyledons. The next stage is called the Torpedo stage and involves the growth of several key structures, including: the radicle (embryotic root), the epicotyl (embryotic stem), and the hypocotyl, (the root/shoot junction). In the final step vascular tissue develops around the seed.
The ovary, inside which the seed is forming from the ovule, grows into a fruit.
All the other main floral parts die during this development, including:
the style, stigma, sepals, stamens, and petals. The fruit contains
three structures: the exocarp, or outer layer, the mesocarp, or the fleshy part, and the endocarp, or innermost layer, while the fruit wall is called the pericarp.
The size, shape, toughness, and thickness varies among different fruit.
This is because it is directly connected to the method of seed
dispersal; that being the purpose of fruit - to encourage or enable the
seed's dispersal and protect the seed while doing so.
Following the pollination of a flower, fertilization, and finally the
development of a seed and fruit, a mechanism is typically used to
disperse the fruit away from the plant.
In Angiosperms (flowering plants) seeds are dispersed away from the
plant so as to not force competition between the mother and the daughter
plants,
as well as to enable the colonisation of new areas. They are often
divided into two categories, though many plants fall in between or in
one or more of these:
Allochory
In allochory, plants use an external vector, or carrier, to transport their seeds away from them. These can be either biotic (living), such as by birds and ants, or abiotic (non-living), such as by the wind or water.
Many plants use biotic vectors to disperse their seeds away from them. This method falls under the umbrella term Zoochory, while Endozoochory, also known as fruigivory,
refers specifically to plants adapted to grow fruit in order to attract
animals to eat them. Once eaten they go through typically go through
animal's digestive system and are dispersed away from the plant. Some seeds are specially adapted either to last in the gizzard of animals or even to germinate better after passing through them. They can be eaten by birds (ornithochory), bats (chiropterochory), rodents, primates, ants (myrmecochory), non-bird sauropsids (saurochory), mammals in general (mammaliochory), and even fish.
Typically their fruit are fleshy, have a high nutritional value, and
may have chemical attractants as an additional "reward" for dispersers.
This is reflected morphologically in the presence of more pulp, an aril, and sometimes an elaiosome (primarily for ants), which are other fleshy structures.
Epizoochory occurs in plants whose seeds are adapted to cling on to animals and be dispersed that way, such as many species in the genus Acaena. Typically these plants seed's have hooks or a viscous surface to easier grip to animals, which include birds and animals with fur. Some plants use mimesis, or imitation, to trick animals into dispersing the seeds and these often have specially adapted colors.
The final type of Zoochory is called Synzoochory,
which involves neither the digestion of the seeds, nor the
unintentional carrying of the seed on the body, but the deliberate
carrying of the seeds by the animals. This is usually in the mouth or beak of the animal (called Stomatochory), which is what is used for many birds and all ants.
In abiotic dispersal plants use the vectors of the wind, water, or a
mechanism of their own to transport their seeds away from them. Anemochory
involves using the wind as a vector to disperse plant's seeds. Because
these seeds have to travel in the wind they are almost always small -
sometimes even dust-like, have a high surface-area-to-volume ratio, and are produced in a large number - sometimes up to a million. Plants such as tumbleweeds
detach the entire shoot to let the seeds roll away with the wind.
Another common adaptation are wings, plumes or balloon like structures
that let the seeds stay in the air for longer and hence travel farther.
In Hydrochory plants are adapted to disperse their seeds through bodies of water and so typically are buoyant and have a low relative density with regards to the water. Commonly seeds are adapted morphologically with hydrophobic surfaces, small size, hairs, slime, oil, and sometimes air spaces within the seeds.
These plants fall into three categories: ones where seeds are dispersed
on the surface of water currents, under the surface of water currents,
and by rain landing on a plant.
In autochory,
plants create their own vectors to transport the seeds away from them.
Adaptations for this usually involve the fruits exploding and forcing
the seeds away ballistically, such as in Hura crepitans, or sometimes in the creation of creeping diaspores.
Because of the relatively small distances that these methods can
disperse their seeds, they are often paired with an external vector.
While land plants have existed for about 425 million years, the first ones reproduced by a simple adaptation of their aquatic counterparts: spores. In the sea, plants—and some animals—can simply scatter out genetic clones
of themselves to float away and grow elsewhere. This is how early
plants reproduced. But plants soon evolved methods of protecting these
copies to deal with drying out and other damage which is even more
likely on land than in the sea. The protection became the seed, though it had not yet evolved the flower. Early seed-bearing plants include the ginkgo and conifers.
Archaefructus liaoningensis, one of the earliest known flowering plants
Several groups of extinct gymnosperms, particularly seed ferns,
have been proposed as the ancestors of flowering plants but there is no
continuous fossil evidence showing exactly how flowers evolved. The
apparently sudden appearance of relatively modern flowers in the fossil
record posed such a problem for the theory of evolution that it was
called an "abominable mystery" by Charles Darwin.
Recently discovered angiosperm fossils such as Archaefructus,
along with further discoveries of fossil gymnosperms, suggest how
angiosperm characteristics may have been acquired in a series of steps.
An early fossil of a flowering plant, Archaefructus liaoningensis from China, is dated about 125 million years old. Even earlier from China is the 125–130 million years old Archaefructus sinensis. In 2015 a plant (130 million-year-old Montsechia vidalii, discovered in Spain) was claimed to be 130 million years old. In 2018, scientists reported that the earliest flowers began about 180 million years ago.
Amborella trichopoda may have characteristic features of the earliest flowering plants
Recent DNA analysis (molecular systematics) shows that Amborella trichopoda, found on the Pacific island of New Caledonia, is the only species in the sister group
to the rest of the flowering plants, and morphological studies suggest
that it has features which may have been characteristic of the earliest
flowering plants.
Besides the hard proof of flowers in or shortly before the Cretaceous,
there is some circumstantial evidence of flowers as much as 250 million
years ago. A chemical used by plants to defend their flowers, oleanane, has been detected in fossil plants that old, including gigantopterids,
which evolved at that time and bear many of the traits of modern,
flowering plants, though they are not known to be flowering plants
themselves, because only their stems and prickles have been found
preserved in detail; one of the earliest examples of petrification.
The similarity in leaf and stem
structure can be very important, because flowers are genetically just
an adaptation of normal leaf and stem components on plants, a
combination of genes normally responsible for forming new shoots.
The most primitive flowers are thought to have had a variable number of
flower parts, often separate from (but in contact with) each other. The
flowers would have tended to grow in a spiral pattern, to be bisexual (in plants, this means both male and female parts on the same flower), and to be dominated by the ovary
(female part). As flowers grew more advanced, some variations developed
parts fused together, with a much more specific number and design, and
with either specific sexes per flower or plant, or at least "ovary
inferior".
The general assumption is that the function of flowers, from the
start, was to involve animals in the reproduction process. Pollen can be
scattered without bright colors and obvious shapes, which would
therefore be a liability, using the plant's resources, unless they
provide some other benefit. One proposed reason for the sudden, fully
developed appearance of flowers is that they evolved in an isolated
setting like an island, or chain of islands, where the plants bearing
them were able to develop a highly specialized relationship with some
specific animal (a wasp, for example), the way many island species
develop today. This symbiotic relationship, with a hypothetical wasp
bearing pollen from one plant to another much the way fig wasps do today, could have eventually resulted in both the plant(s) and their partners developing a high degree of specialization. Island genetics is believed to be a common source of speciation,
especially when it comes to radical adaptations which seem to have
required inferior transitional forms. Note that the wasp example is not
incidental; bees, apparently evolved specifically for symbiotic plant
relationships, are descended from wasps.
Likewise, most fruit
used in plant reproduction comes from the enlargement of parts of the
flower. This fruit is frequently a tool which depends upon animals
wishing to eat it, and thus scattering the seeds it contains.
While many such symbiotic relationships
remain too fragile to survive competition with mainland organisms,
flowers proved to be an unusually effective means of production,
spreading (whatever their actual origin) to become the dominant form of
land plant life.
Flower evolution continues to the present day; modern flowers
have been so profoundly influenced by humans that many of them cannot be
pollinated in nature. Many modern, domesticated flowers used to be
simple weeds, which only sprouted when the ground was disturbed. Some of
them tended to grow with human crops, and the prettiest did not get
plucked because of their beauty, developing a dependence upon and
special adaptation to human affection.
Reflectance spectra for the flowers of several varieties of rose.
A red rose absorbs about 99.7% of light across a broad area below the
red wavelengths of the spectrum, leading to an exceptionally pure
red. A yellow rose will reflect about 5% of blue light, producing an
unsaturated yellow (a yellow with a degree of white in it).
Many flowering plants reflect as much light as possible within the range of visible wavelengths
of the pollinator the plant intends to attract. Flowers that reflect
the full range of visible light are generally perceived as white
by a human observer. An important feature of white flowers is that they
reflect equally across the visible spectrum. While many flowering
plants use white to attract pollinators, the use of color is also
widespread (even within the same species). Color allows a flowering
plant to be more specific about the pollinator it seeks to attract. The
color model used by human color reproduction technology (CMYK)
relies on the modulation of pigments that divide the spectrum into
broad areas of absorption. Flowering plants by contrast are able to
shift the transition point wavelength between absorption and reflection.
If it is assumed that the visual systems of most pollinators view the
visible spectrum as circular
then it may be said that flowering plants produce color by absorbing
the light in one region of the spectrum and reflecting the light in the
other region. With CMYK, color is produced as a function of the
amplitude of the broad regions of absorption. Flowering plants by
contrast produce color by modifying the frequency (or rather wavelength)
of the light reflected. Most flowers absorb light in the blue to yellow
region of the spectrum and reflect light from the green to red region
of the spectrum. For many species of flowering plant, it is the
transition point that characterizes the color that they produce. Color
may be modulated by shifting the transition point between absorption and
reflection and in this way a flowering plant may specify which
pollinator it seeks to attract. Some flowering plants also have a
limited ability to modulate areas of absorption. This is typically not
as precise as control over wavelength. Humans observers will perceive
this as degrees of saturation (the amount of white in the color).
Carl Linnaeus's method for classifying plants focused solely on the structure and nature of the flowers.
In plant taxonomy, which is the study of the classification and identification of plants, the morphology
of plant's flowers are used extensively – and have been for thousands
of years. Although the history of plant taxonomy extends back to at
least around 300 B.C. with the writings of Theophrastus, the foundation of the modern science is based on works in the 18th and 19th centuries.
Carl Linnaeus
(1707–1778), was a Swedish botanist who spent most of his working life
as a professor of natural history. His landmark 1757 book Species Plantarum lays out his system of classification as well as the concept of binomial nomenclature, the latter of which is still used around the world today. He identified 24 classes, based mainly on the number, length and union of the stamens. The first ten classes follow the number of stamens directly (Octandria have 8 stamens etc.),
while class eleven has 11-20 stamens and classes twelve and thirteen
have 20 stamens; differing only in their point of attachment. The next
five classes deal with the length of the stamens and the final five with
the nature of the reproductive capability of the plant; where the
stamen grows; and if the flower is concealed or exists at all (such as
in ferns). This method of classification, despite being artificial, was used extensively for the following seven decades, before being replaced by the system of another botanist.
Antoine Laurent de Jussieu (1748–1836) was a French botanist whose 1787 work Genera plantarum: secundum ordines naturales disposita
set out a new method for classifying plants; based instead on natural
characteristics. Plants were divided by the number, if any, of cotyledons, and the location of the stamens. The next most major system of classification came in the late 19th century from the botanists Joseph Dalton Hooker (1817–1911) and George Bentham (1800–1884). They built on the earlier works of de Jussieu and Augustin Pyramus de Candolle and devised a system which is still used in many of the world's herbaria.
Plants were divided at the highest level by the number of cotyledons
and the nature of the flowers, before falling into orders (families), genera, and species. This system of classification was published in their Genera plantarum in three volumes between 1862 and 1883. It is the most highly regarded and deemed the "best system of classification," in some settings.
Many flowers have important symbolic meanings in Western culture. The practice of assigning meanings to flowers is known as floriography. Some of the more common examples include:
Red roses are given as a symbol of love, beauty, and passion.
Poppies are a symbol of consolation in time of death. In the United Kingdom, New Zealand, Australia and Canada, red poppies are worn to commemorate soldiers who have died in times of war.
Irises/Lily
are used in burials as a symbol referring to "resurrection/life". It is
also associated with stars (sun) and its petals blooming/shining.
Because of their varied and colorful appearance, flowers have long
been a favorite subject of visual artists as well. Some of the most
celebrated paintings from well-known painters are of flowers, such as Van Gogh's sunflowers series or Monet's water lilies. Flowers are also dried, freeze dried and pressed in order to create permanent, three-dimensional pieces of floral art.
Their symbolism in dreams has also been discussed, with possible interpretations including "blossoming potential".
The Roman goddess of flowers, gardens, and the season of Spring is Flora. The Greek goddess of spring, flowers and nature is Chloris.
In Hindu
mythology, flowers have a significant status. Vishnu, one of the three
major gods in the Hindu system, is often depicted standing straight on a
lotus flower. Apart from the association with Vishnu, the Hindu tradition also considers the lotus to have spiritual significance. For example, it figures in the Hindu stories of creation.
History shows that flowers have been used by humans for thousands of
years, to serve a variety of purposes. An early example of this is from
about 4,500 years ago in Ancient Egypt, where flowers would be used to decorate women's hair. Flowers have also inspired art time and time again, such as in Monet's Water Lilies or William Wordsworth's poem about daffodils entitled: "I Wandered Lonely as a Cloud".
In modern times, people have sought ways to cultivate, buy, wear,
or otherwise be around flowers and blooming plants, partly because of
their agreeable appearance and smell. Around the world, people use flowers to mark important events in their lives:
A woman spreading flowers over a lingam in a temple in Varanasi
Flowers collected for worship of Hindu deities in morning, in West Bengal.
Flowers like jasmine
have been used as a replacement for traditional tea in China for
centuries. Most recently many other herbs and flowers used traditionally
across the world are gaining importance to preapare a range of floral tea.
People therefore grow flowers around their homes, dedicate parts of their living space to flower gardens, pick wildflowers, or buy commercially-grown flowers from florists.
Flowers provide less food than other major plant parts (seeds, fruits, roots, stems and leaves), but still provide several important vegetables and spices. Flower vegetables include broccoli, cauliflower and artichoke. The most expensive spice, saffron, consists of dried stigmas of a crocus. Other flower spices are cloves and capers. Hops flowers are used to flavor beer. Marigold flowers are fed to chickens
to give their egg yolks a golden yellow color, which consumers find
more desirable; dried and ground marigold flowers are also used as a
spice and colouring agent in Georgian cuisine. Flowers of the dandelion and elder are often made into wine. Bee pollen, pollen collected from bees, is considered a health food by some people. Honey consists of bee-processed flower nectar and is often named for the type of flower, e.g. orange blossom honey, clover honey and tupelo honey.
Flowers such as chrysanthemum, rose, jasmine, Japanese honeysuckle, and chamomile, chosen for their fragrance and medicinal properties, are used as tisanes, either mixed with tea or on their own.
Flowers have been used since prehistoric times in funeral rituals: traces of pollen have been found on a woman's tomb in the El Miron Cave in Spain.
Many cultures draw a connection between flowers and life and death, and
because of their seasonal return flowers also suggest rebirth, which
may explain why many people place flowers upon graves. The ancient Greeks, as recorded in Euripides's play The Phoenician Women, placed a crown of flowers on the head of the deceased; they also covered tombs with wreaths and flower petals. Flowers were widely used in ancient Egyptian burials, and the Mexicans to this day use flowers prominently in their Day of the Dead celebrations in the same way that their Aztec ancestors did.
The flower-giving tradition goes back to prehistoric times when
flowers often had a medicinal and herbal attributes. Archaeologists
found in several grave sites remnants of flower petals. Flowers were
first used as sacrificial and burial objects. Ancient Egyptians and later Greeks and Romans used flowers. In Egypt, burial objects from the time around 1540 BC were found, which depicted red poppy, yellow Araun, cornflower and lilies. Records of flower giving appear in Chinese writings and Egyptian hieroglyphics, as well as in Greek and Roman mythology. The practice of giving a flower flourished in the Middle Ages when couples showed affection through flowers.
The tradition of flower-giving exists in many forms. It is an important part of Russian culture
and folklore. It is common for students to give flowers to their
teachers. To give yellow flowers in a romantic relationship means
break-up in Russia. Nowadays, flowers are often given away in the form
of a flower bouquet.
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