Information

Animal gene in plants


Usually only microbes, specifically bacteria are used to express genes of other species for various functions. But, it is possible to try and express an animal gene into a plant. Bacteria like Bacillus thuringiensis is used in many plants like cotton, to modify them to BT cotton with insecticidal properties. Can one use an animal gene to get those characteristics in the plant?


A few years ago plant scientists introduced a protein (afa3)in tomato from Winter Flounder, a type of fish surviving freezing conditions. The idea was to make a frost resistant tomato but I believe they did not have much success. Anti-GMO activists had a field day however with baseless claims of making tomato's smell like fish and other nonesense.


One example that I am aware of where an animal transgene was put into a plant was to produce the ZMapp, a chimeric, monoclonal antibody against the Ebola virus.

This is a wikipedia article on ZMapp, that gives you an idea of the process.

Other than this, I am not all that familiar with plant transgenics, other than Round Up resistance genes that were transfected from soil bacteria that developed a resistance to the active chemical in Round Up.

Hopefully other answers can provide you with more details, but these are the two examples that I know off the top of my head.


An evolutionary case for functional gene body methylation in plants and animals

Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.

Cytosine methylation is a covalent modification of DNA that is shared by plants, animals, and other eukaryotes [1]. The most frequently methylated sequences in plant genomes are symmetrical CG dinucleotides, and this methylation is maintained across cell divisions by the MET1 family of methyltransferases. Plants also have abundant methylation of cytosines in other (non-CG) sequence contexts, which is catalyzed by the chromomethylases (CMT2 and CMT3) and by the DRM enzymes that are guided by small RNA molecules via the RNA-directed DNA methylation (RdDM) pathway [2, 3].

Methylation in all contexts is located within transposable elements, which are nearly ubiquitously methylated in land plant genomes [1,2,3]. Methylation prevents transposon expression and transposition and is, therefore, essential for plant genome integrity and transcriptional homeostasis [2, 3]. DNA methylation of transposons that are close to or within genes can affect gene expression, in most cases causing silencing [2, 4]. Modulation of this type of methylation can regulate genes during development. For example, selective methylation removal in specialized sex cells activates some genes and silences others, a process that is essential for successful reproduction [4].


Plants’ Reaction to Rain is Close to Panic, Study Shows

Complex chemical signals are triggered when water lands on a plant to help it prepare for the dangers of rain, according to a new study published in the Proceedings of the National Academy of Sciences.

Van Moerkercke et al made the surprising discovery that a plant’s reaction to rain is close to one of panic. Image credit: Anthony, Inspired Images.

In contrast to humans, plants cannot feel pain. However, so-called mechanical stimulation — rain, wind and physical impact from humans and animals — contributes to the activation of a plant’s defense system at a biochemical level. This in turn triggers a stress hormone that, among other things, can lead to the strengthening of a plant’s immune system.

“As to why plants would need to panic when it rains, strange as it sounds, rain is actually the leading cause of disease spreading between plants,” said University of Western Australia’s Professor Harvey Millar, co-author of the study.

“When a raindrop splashes across a leaf, tiny droplets of water ricochet in all directions. These droplets can contain bacteria, viruses, or fungal spores.”

“The sick leaves can act as a catapult and in turn spread smaller droplets with pathogens to plants several feet away. It is possible that the healthy plants close by want to protect themselves,” added study lead author Dr. Olivier Van Aken, a biologist at Lund University.

In lab experiments, Dr. Van Aken, Professor Millar and their colleagues used a common plant spray bottle set on a soft spray.

Arabidopsis thaliana plants were showered once from a distance of 6 inches (15 cm) after which the researchers noticed a chain reaction in the plant caused by a protein called Myc2.

“When Myc2 is activated, thousands of genes spring into action preparing the plant’s defenses,” Professor Millar explained.

“These warning signals travel from leaf to leaf and induce a range of protective effects.”

“Our results show that plants are very sensitive and do not need heavy rain to be affected and alerted at a biochemical level,” Dr. Van Aken said.

The findings also suggest that when it rains, the same signals spreading across leaves are transmitted to nearby plants through the air.

“One of the chemicals produced is a hormone called jasmonic acid that is used to send signals between plants,” Professor Millar said.

“If a plant’s neighbors have their defense mechanisms turned on, they are less likely to spread disease, so it’s in their best interest for plants to spread the warning to nearby plants.”

“When danger occurs, plants are not able to move out of the way so instead they rely on complex signaling systems to protect themselves.”

“It was clear plants had an intriguing relationship with water, with rain a major carrier of disease but also vital for a plant’s survival,” Professor Millar concluded.

Alex Van Moerkercke et al. A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels. PNAS, published online October 29, 2019 doi: 10.1073/pnas.1911758116


Overview

This topic was discussed in the BITN class, Fall 2003. This overview section summarizes the class presentation. The original web materials were designed as a supplement to that class presentation.

Genetic modification. We will discuss some general background, on mutations and recombination. This will lead to work on genetically modified plants and animals -- and gene therapy for humans.

We began to talk about gene modification. We started with the natural processes of mutation and recombination. The former creates new genetic information and the latter rearranges existing information. A generic procedure for gene modification involves getting (finding or making) a new gene, getting it into the desired cell, and getting it to function. All of these steps have many variations, depending both on the specific goal and the organism being modified. I showed examples involving bacteria, tobacco and mice. I showed slides which are equivalent to Figures 7-4, 8-36, and 8-38 from Lodish et al, Molecular Cell Biology (4th edition, 2000). A link to a very nice animation of part of the recombination process is below under New Links.

We discussed the gene therapy trial for X-SCID in some detail. We briefly discussed the nature of the disease, and then the general approach of the gene therapy treatment. The basic result is a very high level of treatment success: most of the treated patients have developed immune systems that seem good, and are now living substantially normally. However, two of the patients developed leukemia. The leukemia itself was treatable, so the benefit seems to outweigh the side effect in this case. The leukemia is now understood to be due to how the gene therapy vector integrated. How to avoid this side effect is a subject of active work. An important question, which can be answered only over time, is whether more patients will develop the leukemia side effect. Despite the side effect, this is the best success for gene therapy so far, after two decades or so of work. Two articles in The Scientist on this gene therapy trial are listed for the topic.

We then discussed some issues of GMO crops. I emphasize that formulating questions is the critical step here good questions can -- ultimately -- be answered. The big problem is with "uneasy feelings" that are not formulated as answerable questions. I also emphasize that you do not need to accept my "biases" (predicted likely answers) for things that have not yet been tested.

Article mentioned in class, about trying to predict which crop modifications are more or less likely to be environmental problems: J F Hancock, A framework for assessing the risk of transgenic crops. BioScience 53:512 5/03. In reading this, I think it is more important at this point to follow his general plan, rather than to agree with him on specifics.


CRISPR Applications in Plants

Are you a food label reader? If so, you may have noticed some of your favorite snacks bear the phrase “partially produced with genetic engineering.” This makes sense, given that the soy lectin and corn syrup used in many foods is probably isolated from plants genetically modified to be resistant to a powerful herbicide, glyphosate. Genes, originally isolated from bacteria, were inserted into crop plants, conferring glyphosate tolerance to the soybeans, corn, and other crops. Then, federal regulations followed: requiring that human food made with these plants be labeled “partially produced with genetic engineering.”

While these genetically modified plants have been around almost 20 years, new tools for plant biologists have yielded new traits for plants. At the Plant and Animal Genomics Conference held recently in San Diego, a topic of great interest was applications of the CRIPSR/Cas9 system to plants.

One brilliant approach to using CRISPR in plants is to edit the family of genes that confers susceptibility to bacterial blight in rice. Bacterial blight in rice, caused by Xanthomonas oryzae pv. oryzae, is a huge problem in Asia and Africa.

“To understand sensitivity to bacterial blight, it is necessary to first understand the biology of the disease process,” explains Bing Yang, Ph.D., associate professor in genetics, development and cell biology at Iowa State University.

“Bacteria that cause the blight have effector proteins (called TALs transcription activator-like) that transcriptionally activate a family of genes in rice, referred to as SWEET genes. We strategized that by mutating the promoter region of the SWEET family of genes, the bacterial TAL proteins would no long be able to bind to the promoter. Being unable to bind to the promoter DNA, the bacterial TAL proteins cannot induce expression of the SWEET genes. Hence, TAL proteins could no longer bring about a state of disease susceptibility in rice,” explains Dr. Yang.

“CRISPR experiments can be designed to leave no fingerprint, or exogenous DNA in the plants. From a regulatory standpoint, the USDA should accept rice plants with small deletions or mutations in their genomes as safe for field tests,” concludes Dr. Yang.

Using a similar approach, disease-resistant citrus trees have also been developed. In Florida, the citrus industry faces disease challenges from citrus canker and citrus greening disease caused by two bacteria, Xanthomonas citri and Candidatus Liberibacter asiaticus, respectively.

“Citrus canker is also a big problem,” asserts Nian Wang, Ph.D., associate professor, department of microbiology and cell science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida. “A specific effector protein from the infecting bacteria binds to the promoter region of the canker susceptibility gene CsLOB1 to induce disease symptoms. By utilizing CRISPR techniques, we can target the promoter region or the coding region of the citrus susceptibility gene to mutate it in such a way to prevent binding of bacterial transducers.”

The CRISPR/Cas9 system can be applied in a manner that leave no exogenous DNA in the citrus, which is very beneficial in getting USDA approval.

“Applying the same strategy for citrus greening disease, we have begun research to identify the key virulence factors and their targets,” continues Dr. Wang. “We are mutating the putative targets using the CRISPR technology. We hope to generate citrus trees resistant to citrus greening disease.”

Another talk at the conference was on gene editing in cereals by Ming Luo, Ph.D., of the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Canberra, Australia. Wheat rust is a huge problem in failure of wheat crops worldwide finding a solution to the problem would be a milestone in addressing world hunger.

“A pilot study of CRISPR efficacy in rice was successful with a knockout of two closely linked genes. In contrast, the homologous CRISPR experiment in wheat did not lead to any mutations,” declares Dr. Luo. “In contrast, using TALEN in wheat yielded results.

“While CRISPR works in rice and barley, CRISPR editing in wheat has not worked in our hands. We conclude that employing TALENs as a gene-editing tool in wheat is more efficient than CRISPR.”

One drawback to the CRISPR/Cas9 system in plants concerns off-target effects. To assess these effects in plants, whole genome sequencing is the current gold standard.

“Recent work in the model organism Arabidopsis, shows that the CRISPR/Cas9 system correctly targets the desired loci in plant genomes,” states Cara Soyars, University of North Carolina doctoral candidate. “This finding contrasts with off-target CRISPR effects in animals where off-target effects are a serious concern. Extrapolating this to other genera of plants, we postulate that modifications to the Cas9 protein to increase specificity of the binding site is not necessary in plants.”

“Plant genomes have many redundant genes. Hence, to effectively knockout a particular pathway of interest, many genes need to be knocked out,” continues Soyars. “Our lab, the Zachary Nimchuk lab, has developed a system that allows entire families of genes to be targeted in one experiment. While the system is predicted to increase the risk of off-target effects, we have shown with whole genome sequencing that there are very few or no off-target effects in Arabidopsis.

“One of our studies necessitated the targeting of 14 genomic loci at once. Using the multiplexed CRISPR/Cas9 system, we had a 33­–92% success rate. Whole genome sequencing also revealed that chromosomal translocation events are extremely rare after genome manipulation in Arabidopsis via CRISPR/Cas9.

“We really do not know why there is such a lower rate of off-target effects in plants when compared to animals,” clarifies Soyars. “Speculatively, plants use nonhomologous recombination whereas animals employ homologous recombination when joining double DNA breaks. Perhaps differences in these repair mechanisms explain the difference in off target effects?”

One advantage of the CRISPR/Cas9 system is the applicability across a wide range of organisms. Editing carried out for research purposes does not require the same level of stringency as those for therapeutic applications. However, any plants or animals undergoing genome editing will need to be carefully vetted.

The regulatory body overseeing this is the Animal and Plant Health Inspection Service (APHIS), which is part of the USDA. APHIS released for comment a policy suggesting a path forward. For now, very small changes [like single base insertion or deletions (2–10 base pairs removed)] do not seem to be of much interest to APHIS.

“The ability to make these tiny changes at a very specific place in the genome is the result of using CRISPR/Cas9 technology in plants,” affirms Jeff Wolt, Ph.D., professor of agronomy at Iowa State University. “In the past, genetic additions to plants included either exogenous genes or even some of the machinery to get the modifications incorporated.

“Dr. Bing screened plants to select the edited gene of interest, while selecting against the inclusion of the CRISPR machinery. Dr. Bing confirmed this with lots of sequencing. His letter of inquiry to APHIS posed the question: will these rice plants be subject to regulation? APHIS responded that the material can be used without regulatory oversight.

“Plant researchers are moving forward cautiously, as the all the wonderful technology from previous methods of transgenic manipulation was not fully realized due to public push-back. We need to ensure that what we are doing is well-communicated and transparent,” expounds Dr. Wolt.

“Plant sciences have lagged behind in adopting new technologies for genome editing for a couple of reasons,” he continues. “First, funding levels are generally lower for plant researchers than studies involving animals. Second, the techniques used to change the genome must go through the cell walls of plants in animals, especially cell lines, it is much simpler to get the components of CRISPR/Cas9 into the cells.”

“Another reason many of the exciting applications of CRISPR in plants are not discussed as often as medical applications,” explains Mark Behlke, M.D, Ph.D., CSO of Integrated DNA Technologies, “is that the development of agricultural applications done by industry is confidential and is not published quickly, or at all. Also, working with crop plant genomes can be more complex than mammalian cells as these species are often polyploid, which makes manipulation of their genomes more complicated. Furthermore, plant genomes often have huge repetitive content.

“On the other hand,” Dr. Behlke continues, “advances in CRISPR/Cas9 technology has made genome manipulation accessible for just about any research lab in the world. One method that is especially promising is the use of a DNA-free system to perform genome engineering in plants. In this sort of system, the RNA guide is bound to recombinant Cas9 protein and added directly into cells as a ribonucleoprotein (RNP) complex, with no use of plasmids or other DNA-based expression cassettes.

“A delivery method of coating gold nanoparticles with plasmids and shooting them into whole animals has worked in cattle vaccinations (‘biolistics’). This approach is already being applied to plants, to get the Cas9 RNP complexes into cells through their tough cell walls,” concludes Dr. Behlke.


RNA Editing

Jean-Claude Farré , . Alejandro Araya , in Methods in Enzymology , 2007

1.2 In vitro and in organello approaches to study mitochondrial RNA editing

The mitochondrial RNA editing process is poorly understood because of the lack of appropriate experimental approaches. Most current studies on mitochondrial gene expression in plant mitochondria were either based on the analysis of intermediate molecules found in vivo or on laborious in vitro approaches. Nevertheless, many interesting insights have been reported by use of in vitro approaches on the promoter function, RNA processing ( Binder et al., 1995 Hanic-Joyce and Gray, 1991 Lupold et al., 1999 Mulligan et al., 1991 Rapp and Stern, 1992 Rapp et al., 1993 ), and the RNA editing mechanism ( Araya et al., 1992 Blanc et al., 1995 Yu and Schuster, 1995 ).

Unlike chloroplasts, the integration of exogenous genes into the mitochondrial genome has not been achieved probably for several reasons: the difficulty to generate site-specific integration of foreign gene, the lack of suitable selection markers, and the fact that mitochondrial function is essential for plant cell survival. In the absence of reliable methods to transform plant mitochondria, two approaches to study RNA editing have been developed: an in vitro RNA editing system from pea shoots and from cauliflower inflorescences ( Neuwirt et al., 2005 Takenaka and Brennicke, 2003 ), described in detail in Chapter 20 (this volume), and an in organello RNA editing system (electrotransformation) from wheat embryos (Farre and Araya, 2001), potato tubers ( Choury et al., 2005 ), and etiolated seedlings of maize and sorghum ( Staudinger and Kempken, 2003 ) described in this chapter.

The electrotransformation consists of transient incorporation of DNA into purified organelles that is mediated by electroporation. This procedure has several advantages: (1) the possibility to use a site-directed mutagenesis approach to dissect out the recognition signal(s) involved in gene expression processes, (2) the possibility to analyze simultaneously a set of mutant genes with a single preparation of purified mitochondria, and (3) unlike in vitro editing system, in organello approach allows access of several molecular events of the gene expression process, such as transcriptional and posttranscriptional mechanisms.

Several assays to transform isolated organelles have been described. Collombet et al. (1997) reported the introduction of plasmid DNA into isolated mice mitochondria by electroporation. By use of an analogous procedure, To et al. (1996) studied the expression of reporter genes in isolated chloroplasts. Finally, Farre and Araya (2001) optimized this procedure by use of wheat mitochondria to obtain a detailed picture of the molecular and biochemical mechanisms occurring during transcription, splicing, and RNA editing. A major finding of this work was that a transgene could be efficiently transcribed when incorporated into mitochondria by electroporation and that the transcripts were faithfully processed and edited.


Inside an Animal Cell

Nucleus

  • The largest organelle within the cell.
  • It is enclosed by two membranes in an envelope.
  • The nucleus contains chromatin, which is the extended form taken by chromosomes during interphase, as well as a nucleolus.
  • Acts as the control centre of the cell.

Endoplasmic Reticulum (ER)

  • A system of flattened membranes called cisternae (mainpoint: I spelt it wrong in the diagram, sorry).
  • It’s a continuous single membrane which is also the nuclear outer-membrane.
  • When ribosomes are found on its surface it’s known as a rough ER and it transports any proteins made by the ribosomes.
Mitochondria diagram

Mitochondria

  • Site of the Krebs Cycle & Electron Transport Chain in Respiration.
  • Surrounded by two membranes, the inner folded forming cristae.
  • Contains ribosomes, a circular DNA molecule and a matrix.
  • A cell can contain anywhere between 1 to a thousand mitochondria.

Ribosomes

  • Very small organelles consisting of a larger and a smaller subunit.
  • Site of protein synthesis.
  • Ribosomes are responsible for making proteins from genetic information given to it by mRNA and taken from the nucleus.

Golgi Body/Apparatus

  • Similar in structure to the endoplasmic reticulum (ER) but is more compact and is made up of flattened sacks.
  • It’s functions include transporting and storing lipids, producing glycoprotein, forming lysosomes and producing secretary enzyme.

Lysosome

  • This contains digestive enzymes from the remainder of the cell and one of its purposes is destroyed old organelles.

Genetic Variation in Meiosis

The gametes produced in meiosis aren’t genetically identical to the starting cell, and they also aren’t identical to one another. As an example, consider the meiosis II diagram above, which shows the end products of meiosis for a simple cell with a diploid number of 2n = 4 chromosomes. The four gametes produced at the end of meiosis II are all slightly different, each with a unique combination of the genetic material present in the starting cell.

As it turns out, there are many more potential gamete types than just the four shown in the diagram, even for a simple cell with with only four chromosomes. This diversity of possible gametes reflects two factors: crossing over and the random orientation of homologue pairs during metaphase of meiosis I.

  • Crossing over. The points where homologues cross over and exchange genetic material are chosen more or less at random, and they will be different in each cell that goes through meiosis. If meiosis happens many times, as it does in human ovaries and testes, crossovers will happen at many different points. This repetition produces a wide variety of recombinant chromosomes, chromosomes where fragments of DNA have been exchanged between homologues.
  • Random orientation of homologue pairs. The random orientation of homologue pairs during metaphase of meiosis I is another important source of gamete diversity.

Figure 4. Chromosome configuration and homologue segregation

What exactly does random orientation mean here? Well, a homologous pair consists of one homologue from your dad and one from your mom, and you have 23 pairs of homologous chromosomes all together, counting the X and Y as homologous for this purpose. During meiosis I, the homologous pairs will separate to form two equal groups, but it’s not usually the case that all the paternal—dad—chromosomes will go into one group and all the maternal—mom—chromosomes into the other.

Instead, each pair of homologues will effectively flip a coin to decide which chromosome goes into which group. In a cell with just two pairs of homologous chromosomes, like the one at right, random metaphase orientation allows for 2 2 = 4 different types of possible gametes. In a human cell, the same mechanism allows for 2 23 = 8,388,608 different types of possible gametes [1] . And that’s not even considering crossovers!

Given those kinds of numbers, it’s very unlikely that any two sperm or egg cells made by a person will be the same. It’s even more unlikely that you and your sister or brother will be genetically identical, unless you happen to be identical twins, thanks to the process of fertilization (in which a unique egg from Mom combines with a unique sperm from Dad, making a zygote whose genotype is well beyond one-in-a-trillion!) [2] .

Meiosis and fertilization create genetic variation by making new combinations of gene variants (alleles). In some cases, these new combinations may make an organism more or less fit (able to survive and reproduce), thus providing the raw material for natural selection. Genetic variation is important in allowing a population to adapt via natural selection and thus survive in the long term.


Animal gene in plants - Biology

By the end of this section, you will be able to do the following:

  • List the features that distinguish the kingdom Animalia from other kingdoms
  • Explain the processes of animal reproduction and embryonic development
  • Describe the roles that Hox genes play in development

Two different groups within the Domain Eukaryota have produced complex multicellular organisms: The plants arose within the Archaeplastida, whereas the animals (and their close relatives, the fungi) arose within the Opisthokonta. However, plants and animals not only have different life styles, they also have different cellular histories as eukaryotes. The opisthokonts share the possession of a single posterior flagellum in flagellated cells, e.g., sperm cells.

Most animals also share other features that distinguish them from organisms in other kingdoms. All animals require a source of food and are therefore heterotrophic, ingesting other living or dead organisms. This feature distinguishes them from autotrophic organisms, such as most plants, which synthesize their own nutrients through photosynthesis. As heterotrophs, animals may be carnivores, herbivores, omnivores, or parasites ((Figure)a,b). As with plants, almost all animals have a complex tissue structure with differentiated and specialized tissues. The necessity to collect food has made most animals motile, at least during certain life stages. The typical life cycle in animals is diplontic (like you, the diploid state is multicellular, whereas the haploid state is gametic, such as sperm or egg). We should note that the alternation of generations characteristic of the land plants is typically not found in animals. In animals whose life histories include several to multiple body forms (e.g., insect larvae or the medusae of some Cnidarians), all body forms are diploid. Animal embryos pass through a series of developmental stages that establish a determined and fixed body plan. The body plan refers to the morphology of an animal, determined by developmental cues.

Figure 1. Heterotrophy. All animals are heterotrophs and thus derive energy from a variety of food sources. The (a) black bear is an omnivore, eating both plants and animals. The (b) heartworm Dirofilaria immitis is a parasite that derives energy from its hosts. It spends its larval stage in mosquitoes and its adult stage infesting the heart of dogs and other mammals, as shown here. (credit a: modification of work by USDA Forest Service credit b: modification of work by Clyde Robinson)

Complex Tissue Structure

Many of the specialized tissues of animals are associated with the requirements and hazards of seeking and processing food. This explains why animals typically have evolved special structures associated with specific methods of food capture and complex digestive systems supported by accessory organs. Sensory structures help animals navigate their environment, detect food sources (and avoid becoming a food source for other animals!). Movement is driven by muscle tissue attached to supportive structures like bone or chitin, and is coordinated by neural communication. Animal cells may also have unique structures for intercellular communication (such as gap junctions). The evolution of nerve tissues and muscle tissues has resulted in animals’ unique ability to rapidly sense and respond to changes in their environment. This allows animals to survive in environments where they must compete with other species to meet their nutritional demands.

The tissues of animals differ from those of the other major multicellular eukaryotes, plants and fungi, because their cells don’t have cell walls. However, cells of animal tissues may be embedded in an extracellular matrix (e.g., mature bone cells reside within a mineralized organic matrix secreted by the cells). In vertebrates, bone tissue is a type of connective tissue that supports the entire body structure. The complex bodies and activities of vertebrates demand such supportive tissues. Epithelial tissues cover and protect both external and internal body surfaces, and may also have secretory functions. Epithelial tissues include the epidermis of the integument, the lining of the digestive tract and trachea, as well as the layers of cells that make up the ducts of the liver and glands of advanced animals, for example. The different types of tissues in true animals are responsible for carrying out specific functions for the organism. This differentiation and specialization of tissues is part of what allows for such incredible animal diversity.

Just as there are multiple ways to be a eukaryote, there are multiple ways to be a multicellular animal. The animal kingdom is currently divided into five monophyletic clades: Parazoa or Porifera (sponges), Placozoa (tiny parasitic creatures that resemble multicellular amoebae), Cnidaria (jellyfish and their relatives), Ctenophora (the comb jellies), and Bilateria (all other animals). The Placozoa (“flat animal”) and Parazoa (“beside animal”) do not have specialized tissues derived from germ layers of the embryo although they do possess specialized cells that act functionally like tissues. The Placozoa have only four cell types, while the sponges have nearly two dozen. The three other clades do include animals with specialized tissues derived from the germ layers of the embryo. In spite of their superficial similarity to Cnidarian medusae, recent molecular studies indicate that the Ctenophores are only distantly related to the Cnidarians, which together with the Bilateria constitute the Eumetazoa (“true animals”). When we think of animals, we usually think of Eumetazoa, since most animals fall into this category.

Link to Learning

Watch a presentation by biologist E.O. Wilson on the importance of diversity.

Animal Reproduction and Development

Most animals are diploid organisms, meaning that their body (somatic) cells are diploid and haploid reproductive (gamete) cells are produced through meiosis. Some exceptions exist: for example, in bees, wasps, and ants, the male is haploid because it develops from unfertilized eggs. Most animals undergo sexual reproduction. However, a few groups, such as cnidarians, flatworms, and roundworms, may also undergo asexual reproduction, in which offspring originate from part of the parental body.

Processes of Animal Reproduction and Embryonic Development

During sexual reproduction, the haploid gametes of the male and female individuals of a species combine in a process called fertilization. Typically, both male and female gametes are required: the small, motile male sperm fertilizes the typically much larger, sessile female egg. This process produces a diploid fertilized egg called a zygote.

Some animal species—including sea stars and sea anemones—are capable of asexual reproduction. The most common forms of asexual reproduction for stationary aquatic animals include budding and fragmentation, where part of a parent individual can separate and grow into a new individual. This type of asexual reproduction produces genetically identical offspring, which would appear to be disadvantageous from the perspective of evolutionary adaptability, simply because of the potential buildup of deleterious mutations.

In contrast, a form of uniparental reproduction found in some insects and a few vertebrates is called parthenogenesis (or “virgin beginning”). In this case, progeny develop from a gamete, but without fertilization. Because of the nutrients stored in eggs, only females produce parthenogenetic offspring. In some insects, unfertilized eggs develop into new male offspring. This type of sex determination is called haplodiploidy, since females are diploid (with both maternal and paternal chromosomes) and males are haploid (with only maternal chromosomes). A few vertebrates, e.g., some fish, turkeys, rattlesnakes, and whiptail lizards, are also capable of parthenogenesis. In the case of turkeys and rattlesnakes, parthenogenetically reproducing females also produce only male offspring, but not because the males are haploid. In birds and rattlesnakes, the female is the heterogametic (ZW) sex, so the only surviving progeny of post-meiotic parthenogenesis would be ZZ males. In the whiptail lizards, on the other hand, only female progeny are produced by parthenogenesis. These animals may not be identical to their parent, although they have only maternal chromosomes. However, for animals that are limited in their access to mates, uniparental reproduction can ensure genetic propagation.

In animals, the zygote progresses through a series of developmental stages, during which primary germ layers (ectoderm, endoderm, and mesoderm) are established and reorganize to form an embryo. During this process, animal tissues begin to specialize and organize into organs and organ systems, determining their future morphology and physiology.

Animal development begins with cleavage, a series of mitotic cell divisions, of the zygote ((Figure)). Cleavage differs from somatic cell division in that the egg is subdivided by successive cleavages into smaller and smaller cells, with no actual cell growth. The cells resulting from subdivision of the material of the egg in this way are called blastomeres. Three cell divisions transform the single-celled zygote into an eight-celled structure. After further cell division and rearrangement of existing cells, a solid morula is formed, followed by a hollow structure called a blastula. The blastula is hollow only in invertebrates whose eggs have relatively small amounts of yolk. In very yolky eggs of vertebrates, the yolk remains undivided, with most cells forming an embryonic layer on the surface of the yolk (imagine a chicken embryo growing over the egg’s yolk), which serve as food for the developing embryo.

Further cell division and cellular rearrangement leads to a process called gastrulation. Gastrulation results in two important events: the formation of the primitive gut (archenteron) or digestive cavity, and the formation of the embryonic germ layers, as we have discussed above. These germ layers are programmed to develop into certain tissue types, organs, and organ systems during a process called organogenesis. Diploblastic organisms have two germ layers, endoderm and ectoderm. Endoderm forms the wall of the digestive tract, and ectoderm covers the surface of the animal. In triploblastic animals, a third layer forms: mesoderm, which differentiates into various structures between the ectoderm and endoderm, including the lining of the body cavity.

Figure 2. Development of a simple embryo. During embryonic development, the zygote undergoes a series of mitotic cell divisions, or cleavages, that subdivide the egg into smaller and smaller blastomeres. Note that the 8-cell stage and the blastula are about the same size as the original zygote. In many invertebrates, the blastula consists of a single layer of cells around a hollow space. During a process called gastrulation, the cells from the blastula move inward on one side to form an inner cavity. This inner cavity becomes the primitive gut (archenteron) of the gastrula (“little gut”) stage. The opening into this cavity is called the blastopore, and in some invertebrates it is destined to form the mouth.

Some animals produce larval forms that are different from the adult. In insects with incomplete metamorphosis, such as grasshoppers, the young resemble wingless adults, but gradually produce larger and larger wing buds during successive molts, until finally producing functional wings and sex organs during the last molt. Other animals, such as some insects and echinoderms, undergo complete metamorphosis in which the embryo develops into one or more feeding larval stages that may differ greatly in structure and function from the adult ((Figure)). The adult body then develops from one or more regions of larval tissue. For animals with complete metamorphosis, the larva and the adult may have different diets, limiting competition for food between them. Regardless of whether a species undergoes complete or incomplete metamorphosis, the series of developmental stages of the embryo remains largely the same for most members of the animal kingdom.

Figure 3. Insect metamorphosis. (a) The grasshopper undergoes incomplete metamorphosis. (b) The butterfly undergoes complete metamorphosis. (credit: S.E. Snodgrass, USDA)

Link to Learning

Watch the following video to see how human embryonic development (after the blastula and gastrula stages of development) reflects evolution.

The Role of Homeobox (Hox) Genes in Animal Development

Since the early nineteenth century, scientists have observed that many animals, from the very simple to the complex, shared similar embryonic morphology and development. Surprisingly, a human embryo and a frog embryo, at a certain stage of embryonic development, look remarkably alike! For a long time, scientists did not understand why so many animal species looked similar during embryonic development but were very different as adults. They wondered what dictated the developmental direction that a fly, mouse, frog, or human embryo would take. Near the end of the twentieth century, a particular class of genes was discovered that had this very job. These genes that determine animal structure are called “homeotic genes,” and they contain DNA sequences called homeoboxes. Genes with homeoboxes encode protein transcription factors. One group of animal genes containing homeobox sequences is specifically referred to as Hox genes. This cluster of genes is responsible for determining the general body plan, such as the number of body segments of an animal, the number and placement of appendages, and animal head-tail directionality. The first Hox genes to be sequenced were those from the fruit fly (Drosophila melanogaster). A single Hox mutation in the fruit fly can result in an extra pair of wings or even legs growing from the head in place of antennae (this is because antennae and legs are embryologic homologous structures and their appearance as antennae or legs is dictated by their origination within specific body segments of the head and thorax during development). Now, Hox genes are known from virtually all other animals as well.

While there are a great many genes that play roles in the morphological development of an animal, including other homeobox-containing genes, what makes Hox genes so powerful is that they serve as “master control genes” that can turn on or off large numbers of other genes. Hox genes do this by encoding transcription factors that control the expression of numerous other genes. Hox genes are homologous across the animal kingdom, that is, the genetic sequences of Hox genes and their positions on chromosomes are remarkably similar across most animals because of their presence in a common ancestor, from worms to flies, mice, and humans ((Figure)). In addition, the order of the genes reflects the anterior-posterior axis of the animal’s body. One of the contributions to increased animal body complexity is that Hox genes have undergone at least two and perhaps as many as four duplication events during animal evolution, with the additional genes allowing for more complex body types to evolve. All vertebrates have four (or more) sets of Hox genes, while invertebrates have only one set.

Art Connection

Figure 4. Hox genes. Hox genes are highly conserved genes encoding transcription factors that determine the course of embryonic development in animals. In vertebrates, the genes have been duplicated into four clusters on different chromosomes: Hox-A, Hox-B, Hox-C, and Hox-D. Genes within these clusters are expressed in certain body segments at certain stages of development. Shown here is the homology between Hox genes in mice and humans. Note how Hox gene expression, as indicated with orange, pink, blue, and green shading, occurs in the same body segments in both the mouse and the human. While at least one copy of each Hox gene is present in humans and other vertebrates, some Hox genes are missing in some chromosomal sets.

If a Hox 13 gene in a mouse was replaced with a Hox 1 gene, how might this alter animal development?

Two of the five clades within the animal kingdom do not have Hox genes: the Ctenophora and the Porifera. In spite of the superficial similarities between the Cnidaria and the Ctenophora, the Cnidaria have a number of Hox genes, but the Ctenophora have none. The absence of Hox genes from the ctenophores has led to the suggestion that they might be “basal” animals, in spite of their tissue differentiation. Ironically, the Placozoa, which have only a few cell types, do have at least one Hox gene. The presence of a Hox gene in the Placozoa, in addition to similarities in the genomic organization of the Placozoa, Cnidaria and Bilateria, has led to the inclusion of the three groups in a “Parahoxozoa” clade. However, we should note that at this time the reclassification of the Animal Kingdom is still tentative and requires much more study.

The animal might develop two heads and no tail.

Section Summary

Animals constitute an incredibly diverse kingdom of organisms. Although animals range in complexity from simple sea sponges to human beings, most members of the animal kingdom share certain features. Animals are eukaryotic, multicellular, heterotrophic organisms that ingest their food and usually develop into motile creatures with a fixed body plan. A major characteristic unique to the animal kingdom is the presence of differentiated tissues, such as nerve, muscle, and connective tissues, which are specialized to perform specific functions. Most animals undergo sexual reproduction, leading to a series of developmental embryonic stages that are relatively similar across the animal kingdom. A class of transcriptional control genes called Hox genes directs the organization of the major animal body plans, and these genes are strongly homologous across the animal kingdom.

Art Connections

(Figure) If a Hox 13 gene in a mouse was replaced with a Hox 1 gene, how might this alter animal development?


Discussion

An ideal barcode should possess sufficient variation among the sequences to discriminate species however, it also needs to be sufficiently conserved so that there is less variability within species than between species [37], [38]. Chen et al. (2010) compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species and proposed that ITS2 can be potentially used as a standard DNA barcode to identify medicinal plants. The ITS2 region has also been used as a barcode to identify spider mites [41], Sycophila [16], and Fasciola [18]. In the present study, we extended this analysis across all plants and animals, and assessed the species discrimination capacity of ITS2 sequences for 50,790 plant and 12,221 animal sequences (Table S1). The success rates for identification of plants and animals were more than 97% and 74% at the genus and species level (Table 2), respectively, except for gymnosperms, which had a 67.1% success rate at the species level. In addition, the ITS2 region had a high success rate for discriminating between closely related species in plants and animals (Fig. 3, Tables 3, 4, 5, S2, and S3). The sequence length of ITS2 is short (Fig. 1), which satisfies the requirements for PCR amplification and sequencing. Finally, the secondary structures of ITS2 are conserved and can provide useful biological information for alignment [2], [4], [35] thus, it can be considered as molecular morphological characteristics for species identification.

The ITS2 sequence lengths of plants and animals were mainly distributed in the 195–510 bp range. The identification of plant and animal voucher species and other collections using DNA barcoding techniques is one of the main tasks in natural museums and research institutes. The length of the ITS2 region is sufficiently short to allow amplification of even degraded DNA. In addition, the intra-specific variations in plants and animals are lower than the inter-specific divergences. But the overlap of genetic variation without barcoding gaps significantly increases when the number of closely related species is increased [32].

Hebert et al. found that more than 98% of 13,320 congeneric species pairs, including representatives from 11 phyla, have sufficient sequence divergence to ensure easy identification [20]. However, the sequence divergence of COI for some animal species, such as cnidarians [20] and the West Palaearctic Pandasyopthalmus taxa [39], is relatively low, and even invariant. In addition, mtDNA is maternally inherited other resources of data should be considered, such as nuclear DNA, morphology, or ecology [40]. The success rate of using ITS2 for identification of animals is 91.7% at the species level based on testing of a comprehensive sample set, and the identification efficiency of ITS2 for sequences in cnidarians is more than 77%. ITS2 sequences have a relatively high divergence rate thus, it can be used as a complementary locus to CO1 for identification of animal species.

Recently, ITS2 region has been found to vary in primary sequences and secondary structures in a way that correlates highly with taxonomic classification. Several researchers have already demonstrated the potential for using ITS2 for taxonomic classification and phylogenetic reconstruction at both the genus and species levels for eukaryotes, including animals, plants, and fungi [2], [4], [8], [9], [42], [43]. The ITS2 region of nuclear DNA provides a powerful tool because of sufficient variation in primary sequences and secondary structures. Analysis of the secondary structures formed by the RNA transcript as it folds back upon itself at transcription has been less commonly conducted however, it has been proven extremely useful in aiding proper sequence alignment [1], [44]. Schultz and Wolf described the utilization of ITS2′s primary sequence and secondary structure information, together with an ITS2-specific scoring matrix and an ITS2-specific substitution model, based on tools such as 4SALE, the CBCAnalyzer, and ProfDistS [9].

Among of 50,790 ITS2 sequences of plants and 12,221 ITS2 sequences of animals,139 and 30 sequences, respectively, could be fungal sequences. Thus, the frequency is less than 0.3% in both plants and animals. This result is similar to that of Chen et al. [11]. The frequency of suspected fungal sequences in monocotyledon ITS2 sequences is twice as high as in dicotyledons, which may be due to the presence of endophytic fungi in most monocotyledon species. Although the rate of fungal contamination is very low, we should pay more attention to the data from the public database [11].

There are multiple copies of ITS (containing ITS1 and ITS2) in plants and animals. Although different copies of ITS exist, which may result in misleading phylogenetic inferences [45], there remain several advantages for its widespread use, such as the levels of variations and multicopy structure facilitating PCR amplification, even from herbarium specimens [46].

In conclusion, we believe that the ITS2 locus can be used as a barcode for authenticating plant species, as well as a complementary locus to CO1 for identifying animal species. The sequences of the universal primers and the amplification conditions for obtaining the ITS2 sequences of plants and animals can be found in Table S5, as well as in the ITS2 application web. There were limited ITS2 sequences of ferns and vertebrates in the GenBank therefore, the success rates for ITS2 to identify them need further investigation.


Watch the video: Top 7 Genetically Modified Animals (December 2021).