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84-398: See text Isoetes , commonly known as the quillworts , is a genus of lycopod . It is the only living genus in the family Isoetaceae and order Isoetales . There are currently [when?] 192 recognized species, with a cosmopolitan distribution mostly in aquatic habitats but with the individual species often scarce to rare. Species virtually identical to modern quillworts have existed since

168-452: A century and it is likely that they are more abundant than coding DNA. Telomeres are regions of repetitive DNA at the end of a chromosome , which provide protection from chromosomal deterioration during DNA replication . Recent studies have shown that telomeres function to aid in its own stability. Telomeric repeat-containing RNA (TERRA) are transcripts derived from telomeres. TERRA has been shown to maintain telomerase activity and lengthen

252-406: A few (e.g. I. tegetiformans ) form spreading mats. This swollen base also contains male and female sporangia, protected by a thin, transparent covering ( velum ), which is used diagnostically to help identify quillwort species. They are heterosporous . Quillwort species are very difficult to distinguish by general appearance. The best way to identify them is by examining their megaspores under

336-403: A large proportion of the genomic sequences in many species. Alu sequences , classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. Some examples have been found of SINEs exerting transcriptional control of some protein-encoding genes. Endogenous retrovirus sequences are the product of reverse transcription of retrovirus genomes into

420-403: A microscope. Moreover, habitat, texture, spore size, and velum provide features that distinguish Isoëtes taxa. They also possess a vestigial form of secondary growth in the basal portions of its cormlike stem, an indication that they evolved from larger ancestors. Quillworts use crassulacean acid metabolism (CAM) for carbon fixation. Some aquatic species do not have stomata and the leaves have

504-595: A modified shoot system acting as roots, bipolar and secondary growth , and an upright stance. The remains of Lepidodendron lycopods formed many fossil coal deposits. In Fossil Grove , Victoria Park, Glasgow, Scotland, fossilized lycophytes can be found in sandstone . The Lycopodiopsida had their maximum diversity in the Pennsylvanian (Upper Carboniferous), particularly tree-like Lepidodendron and Sigillaria that dominated tropical wetlands. The complex ecology of these tropical rainforests collapsed during

588-527: A more broadly defined taxon of lycophytes that includes some extinct groups more distantly related to extant lycophytes, such as the zosterophylls . For example, Kenrick & Crane (1997) use the subdivision Lycophytina for this purpose, with all extant lycophytes falling within the class Lycopsida. Other sources exclude the zosterophylls from any "lycophyte" taxon. In the Pteridophyte Phylogeny Group classification of 2016 (PPG I),

672-410: A number of unique RNA genes that produce catalytic RNAs . Noncoding genes account for only a few percent of prokaryotic genomes but they can represent a vastly higher fraction in eukaryotic genomes. In humans, the noncoding genes take up at least 6% of the genome, largely because there are hundreds of copies of ribosomal RNA genes. Protein-coding genes occupy about 38% of the genome; a fraction that

756-519: A result of ingestion ( endozoochory ). These are among the reasons suggested for the ornamentations of the spore, with some authors demonstrating that certain patterns seem well-adapted for sticking to relevant animals like waterfowl. Another critical element of dispersal is the observation that in some species of Isoetes , the outer coat of megaspores have pockets that trap microspores, a condition known as synaptospory. Typically, heterospory means that colonization and long-dispersal are more difficult due to

840-414: A simple repeat such as ATC. There are about 350,000 STRs in the human genome and they are scattered throughout the genome with an average length of about 25 repeats. Variations in the number of STR repeats can cause genetic diseases when they lie within a gene but most of these regions appear to be non-functional junk DNA where the number of repeats can vary considerably from individual to individual. This

924-464: A substantial proportion of the genome. In humans, for example, introns in protein-coding genes cover 37% of the genome. Combining that with about 1% coding sequences means that protein-coding genes occupy about 38% of the human genome. The calculations for noncoding genes are more complicated because there is considerable dispute over the total number of noncoding genes but taking only the well-defined examples means that noncoding genes occupy at least 6% of

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1008-554: A thick cuticle which prevents CO 2 uptake, a task that is performed by their hollow roots instead, which absorb CO 2 from the sediment. This has been studied extensively in Isoetes andicola . CAM is normally considered an adaptation to life in arid environments to prevent water loss with the plants opening their stomata at night rather than in the heat of the day. This allows CO 2 to enter and minimises water loss. As mostly submerged aquatic plants, quillworts do not lack water and

1092-606: Is an endophytic fungus present in Huperzia serrata that produces Huperzine A , a biomedical compound which has been approved as a drug in China and a dietary supplement in the U.S. to treat Alzheimer's Disease. This fungal endophyte can be cultivated much more easily and on a much larger scale than H. serrata itself which could increase the availability of Huperzine A as a medicine. The spores of lycopods are highly flammable and so have been used in fireworks . Lycopodium powder ,

1176-527: Is called the C-value Enigma. This led to the observation that the number of genes does not seem to correlate with perceived notions of complexity because the number of genes seems to be relatively constant, an issue termed the G-value Paradox . For example, the genome of the unicellular Polychaos dubium (formerly known as Amoeba dubia ) has been reported to contain more than 200 times

1260-418: Is completely absent in seed plants except for Ginkgo and cycads). Because only two flagella puts a size limit on the genome, we find the largest known genomes in the clade in Isoetes , as multiflagellated sperm is not exposed for the same selection pressure as biflagellate sperm in regard of size. The extant lycophytes are vascular plants (tracheophytes) with microphyllous leaves , distinguishing them from

1344-502: Is considerable controversy in the scientific literature. The nonfunctional DNA in bacterial genomes is mostly located in the intergenic fraction of non-coding DNA but in eukaryotic genomes it may also be found within introns . There are many examples of functional DNA elements in non-coding DNA, and it is erroneous to equate non-coding DNA with junk DNA. Genome-wide association studies (GWAS) identify linkages between alleles and observable traits such as phenotypes and diseases. Most of

1428-432: Is currently without an explained origin is expected to have found its origin in transposable elements that were active so long ago (> 200 million years) that random mutations have rendered them unrecognizable. Genome size variation in at least two kinds of plants is mostly the result of retrotransposon sequences. Highly repetitive DNA consists of short stretches of DNA that are repeated many times in tandem (one after

1512-658: Is developed enough for independence is the new plant dropped to the ground. Many club-moss gametophytes are mycoheterotrophic and long-lived, residing underground for several years before emerging from the ground and progressing to the sporophyte stage. Lycopodiaceae and spikemosses ( Selaginella ) are the only vascular plants with biflagellate sperm, an ancestral trait in land plants otherwise only seen in bryophytes . The only exceptions are Isoetes and Phylloglossum , which independently has evolved multiflagellated sperm cells with approximately 20 flagella (sperm flagella in other vascular plants can count at least thousand, but

1596-431: Is due to a reduction in the length of introns and less repetitive DNA. Utricularia gibba , a bladderwort plant, has a very small nuclear genome (100.7 Mb) compared to most plants. It likely evolved from an ancestral genome that was 1,500 Mb in size. The bladderwort genome has roughly the same number of genes as other plants but the total amount of coding DNA comes to about 30% of the genome. The remainder of

1680-425: Is much higher than the coding region because genes contain large introns. The total number of noncoding genes in the human genome is controversial. Some scientists think that there are only about 5,000 noncoding genes while others believe that there may be more than 100,000 (see the article on Non-coding RNA ). The difference is largely due to debate over the number of lncRNA genes. Promoters are DNA segments near

1764-478: Is narrow, 2–20 centimetres (0.8–8 in) long (exceptionally up to 100 cm or 40 in) and 0.5–3.0 mm (0.02–0.12 in) wide; they can be either evergreen , winter deciduous , or dry-season deciduous. Only 4% of total biomass, the tips of the leaves, is chlorophyllous. The roots broaden to a swollen base up to 5 mm (0.2 in) wide where they attach in clusters to a bulb-like, underground rhizome characteristic of most quillwort species, though

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1848-415: Is not known because there are disputes over the number of functional coding exons and over the total size of the human genome. This means that 98–99% of the human genome consists of non-coding DNA and this includes many functional elements such as non-coding genes and regulatory sequences. Genome size in eukaryotes can vary over a wide range, even between closely related species. This puzzling observation

1932-404: Is not powerful enough to eliminate them (see Nearly neutral theory of molecular evolution ). The human genome contains about 15,000 pseudogenes derived from protein-coding genes and an unknown number derived from noncoding genes. They may cover a substantial fraction of the genome (~5%) since many of them contain former intron sequences. Pseudogenes are junk DNA by definition and they evolve at

2016-462: Is unclear because it is difficult to distinguish between spurious transcription factor binding sites and those that are functional. The binding characteristics of typical DNA-binding proteins were characterized in the 1970s and the biochemical properties of transcription factors predict that in cells with large genomes, the majority of binding sites will not be biologically functional. Many regulatory sequences occur near promoters, usually upstream of

2100-494: Is why these length differences are used extensively in DNA fingerprinting . Junk DNA is DNA that has no biologically relevant function such as pseudogenes and fragments of once active transposons. Bacteria and viral genomes have very little junk DNA but some eukaryotic genomes may have a substantial amount of junk DNA. The exact amount of nonfunctional DNA in humans and other species with large genomes has not been determined and there

2184-771: The Induan (earliest Triassic), particularly Pleuromeia . After the worldwide Permian–Triassic extinction event , members of this group pioneered the repopulation of habitats as opportunistic plants. The heterogeneity of the terrestrial plant communities increased markedly during the Middle Triassic when plant groups like horsetails, ferns, pteridosperms , cycads , ginkgos and conifers resurfaced and diversified quickly. Lycophytes form associations with microbes such as fungi and bacteria, including arbuscular mycorrhizal and endophytic associations. Arbuscular mycorrhizal associations have been characterized in all stages of

2268-644: The Jurassic epoch, though the timing of the origin of modern Isoetes is subject to considerable uncertainty. The name of the genus may also be spelled Isoëtes . The diaeresis (two dots over the e) indicates that the o and the e are to be pronounced in two distinct syllables. Including this in print is optional; either spelling ( Isoetes or Isoëtes ) is correct. Quillworts are mostly aquatic or semi-aquatic in clear ponds and slow-moving streams, though several (e.g. I. butleri , I. histrix and I. nuttallii ) grow on wet ground that dries out in

2352-538: The Lycopodiopsida class, are part of the oldest extant lineage that reflects this shift to a sporophyte dominant lifecycle. In closely related lineages, such as the extinct Lepidodendron , spores were dispersed by the sporophyte through large collections of sporangia called strobili for wind-based spore dispersal. However, Isoetes are small heterosporous semi-aquatic plants, with different reproductive needs and challenges than large tree-like land plants. Like

2436-512: The Pteridophyte Phylogeny Group (PPG I), which places them all in the class Lycopodiopsida, which includes the classes Isoetopsida and Selaginellopsida used in other systems. (See Table 2 .) Alternative classification systems have used ranks from division (phylum) to subclass. In the PPG ;I system, the class is divided into three orders, Lycopodiales , Isoetales and Selaginellales . Club-mosses (Lycopodiales) are homosporous, but

2520-537: The euphyllophytes (plants with megaphyllous leaves ). The sister group of the extant lycophytes and their closest extinct relatives are generally believed to be the zosterophylls , a paraphyletic or plesion group. Ignoring some smaller extinct taxa, the evolutionary relationships are as shown below.  (multiple branches, incertae sedis )  living lycophytes and  their extinct close relatives   ferns & horsetails   spermatophytes  (seed plants) As of 2019 , there

2604-416: The 1960s and their general characteristics were worked out in the 1970s by studying specific transcription factors in bacteria and bacteriophage . Promoters and regulatory sequences represent an abundant class of noncoding DNA but they mostly consist of a collection of relatively short sequences so they do not take up a very large fraction of the genome. The exact amount of regulatory DNA in mammalian genome

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2688-479: The 5' end of the gene where transcription begins. They are the sites where RNA polymerase binds to initiate RNA synthesis. Every gene has a noncoding promoter. Regulatory elements are sites that control the transcription of a nearby gene. They are almost always sequences where transcription factors bind to DNA and these transcription factors can either activate transcription (activators) or repress transcription (repressors). Regulatory elements were discovered in

2772-521: The Late Jurassic of North America has been described as the "earliest clear example of a isoetalean lycopsid containing all the major features uniting modern Isoetes", including the loss of the elongated stem and vegetative leaves. Based on this, it has been stated that "the overall morphology of Isoetes appears to have persisted virtually unchanged since at least the Jurassic". The timing of

2856-687: The Lycopodiopsida first appear in the Silurian period, along with a number of other vascular plants. The Silurian Baragwanathia longifolia is one of the earliest identifiable species. Lycopodolica is another Silurian genus which appears to be an early member of this group. The group evolved roots independently from the rest of the vascular plants. From the Devonian onwards, some species grew large and tree-like. Devonian fossil lycopsids from Svalbard , growing in equatorial regions, raise

2940-679: The Middle Pennsylvanian due to a change in climate. In Euramerica , tree-like species apparently became extinct in the Late Pennsylvanian, as a result of a transition to a much drier climate, giving way to conifers , ferns and horsetails . In Cathaysia (now South China), tree-like species survived into the Permian . Nevertheless, lycopodiopsids are rare in the Lopingian (latest Permian), but regained dominance in

3024-460: The RNA transcript is functional (non-coding genes) and regulatory sequences, which means that almost all of the bacterial genome has a function. The amount of coding DNA in eukaryotes is usually a much smaller fraction of the genome because eukaryotic genomes contain large amounts of repetitive DNA not found in prokaryotes. The human genome contains somewhere between 1–2% coding DNA. The exact number

3108-432: The air. The genome sequence also provided two insights into its structure. First, genes and repeated non-coding regions were fairly evenly distributed across all the chromosomes . This is similar to genomes of other non-seed plants, but different from the seed plants ( angiosperms ) where there are distinctly more genes at the ends of chromosomes. Secondly, there was also evidence that the whole genome had been duplicated in

3192-411: The amount of DNA in humans (i.e. more than 600 billion pairs of bases vs a bit more than 3 billion in humans). The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes. Genes take up about 30% of the pufferfish genome and the coding DNA is about 10%. (Non-coding DNA = 90%.) The reduced size of the pufferfish genome

3276-437: The ancient past. Like all land plants, Isoetes undergoes an alternation of generations between a diploid sporophyte stage and a sexual haploid gametophyte stage. However, the dominance of one stage over the other has shifted over time. The development of vascular tissue and subsequent diversification of land plants coincides with the increased dominance of the sporophyte and reduction of the gametophyte. Isoetes , as members of

3360-479: The associations are between single-nucleotide polymorphisms (SNPs) and the trait being examined and most of these SNPs are located in non-functional DNA. The association establishes a linkage that helps map the DNA region responsible for the trait but it does not necessarily identify the mutations causing the disease or phenotypic difference. SNPs that are tightly linked to traits are the ones most likely to identify

3444-495: The dried spores of the common clubmoss, was used in Victorian theater to produce flame-effects. A blown cloud of spores burned rapidly and brightly, but with little heat. (It was considered safe by the standards of the time.) Non-coding DNA In bacteria , the coding regions typically take up 88% of the genome. The remaining 12% does not encode proteins, but much of it still has biological function through genes where

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3528-422: The endangered species I. tegetiformans . Lycopodiopsida See Table 1 . Lycopodiopsida is a class of vascular plants also known as lycopods or lycophytes . Members of the class are also called clubmosses , firmosses , spikemosses and quillworts . They have dichotomously branching stems bearing simple leaves called microphylls and reproduce by means of spores borne in sporangia on

3612-464: The ends of chromosomes. Both prokaryotic and eukarotic genomes are organized into large loops of protein-bound DNA. In eukaryotes, the bases of the loops are called scaffold attachment regions (SARs) and they consist of stretches of DNA that bind an RNA/protein complex to stabilize the loop. There are about 100,000 loops in the human genome and each SAR consists of about 100 bp of DNA, so the total amount of DNA devoted to SARs accounts for about 0.3% of

3696-408: The extant lycophytes (and their closest extinct relatives) varies widely. Table 1 below shows some of the highest ranks that have been used. Systems may use taxa at a rank lower than the highest given in the table with the same circumscription; for example, a system that uses Lycopodiophyta as the highest ranked taxon may place all of its members in a single subclass. Some systems use a higher rank for

3780-534: The extant lycophytes as shown below. Some extinct groups, such as zosterophylls , fall outside the limits of the taxon as defined by the classifications in Table 1 above. However, other extinct groups fall within some circumscriptions of this taxon. Taylor et al. (2009) and Mauseth (2014) include a number of extinct orders in their division (phylum) Lycophyta, although they differ on the placement of some genera. The orders included by Taylor et al. are: Mauseth uses

3864-449: The fact that a single spore cannot grow a bisexual gametophyte and thus cannot establish a new population from a single spore as can happen in homosporous ferns. Isoetes may mitigate this issue via microspores stuck to megaspores, greatly increasing the possibility of successful fertilization upon dispersal. Compared to other genera, Isoetes is poorly known. The first critical monograph on their taxonomy, written by Norma Etta Pfeiffer ,

3948-411: The genera Selaginella (spikemosses) and Isoetes (quillworts) are heterosporous, with female spores larger than the male. As a result of fertilisation, the female gametophyte produces sporophytes. A few species of Selaginella such as S. apoda and S. rupestris are also viviparous ; the gametophyte develops on the mother plant, and only when the sporophyte's primary shoot and root

4032-406: The genome (70% non-coding DNA) consists of promoters and regulatory sequences that are shorter than those in other plant species. The genes contain introns but there are fewer of them and they are smaller than the introns in other plant genomes. There are noncoding genes, including many copies of ribosomal RNA genes. The genome also contains telomere sequences and centromeres as expected. Much of

4116-481: The genome because each centromere can be millions of base pairs in length. In humans, for example, the sequences of all 24 centromeres have been determined and they account for about 6% of the genome. However, it is unlikely that all of this noncoding DNA is essential since there is considerable variation in the total amount of centromeric DNA in different individuals. Centromeres are another example of functional noncoding DNA sequences that have been known for almost half

4200-508: The genome sequence, it appears that in quillworts, both forms are involved in photosynthesis. In addition, circadian expression of key CAM pathway genes peaked at different times of day than in angiosperms. These fundamental differences in biochemistry suggest that CAM in quillworts is probably another example of convergent evolution of CAM during the more than 300 million years since the genus diverged from other plants. However, they may also be because of differences between life in water and in

4284-418: The genome. Centromeres are the sites where spindle fibers attach to newly replicated chromosomes in order to segregate them into daughter cells when the cell divides. Each eukaryotic chromosome has a single functional centromere that is seen as a constricted region in a condensed metaphase chromosome. Centromeric DNA consists of a number of repetitive DNA sequences that often take up a significant fraction of

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4368-504: The genome. The standard biochemistry and molecular biology textbooks describe non-coding nucleotides in mRNA located between the 5' end of the gene and the translation initiation codon. These regions are called 5'-untranslated regions or 5'-UTRs. Similar regions called 3'-untranslated regions (3'-UTRs) are found at the end of the gene. The 5'-UTRs and 3'UTRs are very short in bacteria but they can be several hundred nucleotides in length in eukaryotes. They contain short elements that control

4452-410: The genomes of germ cells . Mutation within these retro-transcribed sequences can inactivate the viral genome. Over 8% of the human genome is made up of (mostly decayed) endogenous retrovirus sequences, as part of the over 42% fraction that is recognizably derived of retrotransposons, while another 3% can be identified to be the remains of DNA transposons . Much of the remaining half of the genome that

4536-536: The genus, separating two South American species into the genus Stylites , although molecular data place these species among other species of Isoetes , so that Stylites does not warrant taxonomic recognition. The earliest fossil that has been assigned to the genus is † Isoetes beestonii from the latest Permian of New South Wales, Australia, around 252 million years ago. However, the relationships of pre-Jurassic isoetaleans to modern Isotetes have been regarded as unclear by other authors. Isoetites rolandii from

4620-442: The human genome. Pseudogenes are mostly former genes that have become non-functional due to mutation, but the term also refers to inactive DNA sequences that are derived from RNAs produced by functional genes ( processed pseudogenes ). Pseudogenes are only a small fraction of noncoding DNA in prokaryotic genomes because they are eliminated by negative selection. In some eukaryotes, however, pseudogenes can accumulate because selection

4704-468: The initiation of translation (5'-UTRs) and transcription termination (3'-UTRs) as well as regulatory elements that may control mRNA stability, processing, and targeting to different regions of the cell. DNA synthesis begins at specific sites called origins of replication . These are regions of the genome where the DNA replication machinery is assembled and the DNA is unwound to begin DNA synthesis. In most cases, replication proceeds in both directions from

4788-690: The junk. Junk is not needed." There are two types of genes : protein coding genes and noncoding genes . Noncoding genes are an important part of non-coding DNA and they include genes for transfer RNA and ribosomal RNA . These genes were discovered in the 1960s. Prokaryotic genomes contain genes for a number of other noncoding RNAs but noncoding RNA genes are much more common in eukaryotes. Typical classes of noncoding genes in eukaryotes include genes for small nuclear RNAs (snRNAs), small nucleolar RNAs (sno RNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and long noncoding RNAs (lncRNAs). In addition, there are

4872-683: The lycophyte lifecycle: mycoheterotrophic gametophyte, photosynthetic surface-dwelling gametophyte, young sporophyte, and mature sporophyte. Arbuscular mycorrhizae have been found in Selaginella spp. roots and vesicles. During the mycoheterotrophic gametophyte lifecycle stage, lycophytes gain all of their carbon from subterranean glomalean fungi. In other plant taxa, glomalean networks transfer carbon from neighboring plants to mycoheterotrophic gametophytes. Something similar could be occurring in Huperzia hypogeae gametophytes which associate with

4956-678: The molecular clock as providing no firm evidence for the origin time of the genus, which could date to the Mesozoic or even the late Paleozoic , depending on the calibration method used. As of November 2019, Plants of the World Online accepted the following extant species: Many species, such as the Louisiana quillwort and the mat-forming quillwort, are endangered species . Several species of Isoetes are commonly called Merlin's grass , especially I. lacustris , but also

5040-427: The motile sperm from a microgametophyte locates the archegonia of a megagametophyte and swims inside to fertilize the egg. Outside of heterospory, a distinguishing feature of Isoetes (and Selaginella ) from other pteridophytes , is that their gametophytes grow inside the spores. This means that the gametophytes never leave the protection of the spore that disperses them, cracking the perispore (the outer layer of

5124-465: The neutral rate as expected for junk DNA. Some former pseudogenes have secondarily acquired a function and this leads some scientists to speculate that most pseudogenes are not junk because they have a yet-to-be-discovered function. Transposons and retrotransposons are mobile genetic elements . Retrotransposon repeated sequences , which include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), account for

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5208-550: The non-coding DNA of animals do not seem to apply to plant genomes. According to a New York Times article, during the evolution of this species, "... genetic junk that didn't serve a purpose was expunged, and the necessary stuff was kept." According to Victor Albert of the University of Buffalo, the plant is able to expunge its so-called junk DNA and "have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without

5292-749: The order †Asteroxylales, placing Baragwanathia in the Protolepidodendrales. The relationship between some of these extinct groups and the extant ones was investigated by Kenrick and Crane in 1997. When the genera they used are assigned to orders, their suggested relationship is: †Drepanophycales († Asteroxylon , † Baragwanathia , † Drepanophycus ) Lycopodiales †Protolepidodendrales († Leclercqia , † Minarodendron ) Selaginellales ( Selaginella , including subg. Stachygynandrum and subg. Tetragonostachys ) Isoetales ( Isoetes ) †Lepidodendrales († Paralycopodites ) The Lycopodiopsida are distinguished from other vascular plants by

5376-425: The origin of the crown group is uncertain. Wood et al (2020) asserted there to be no morphological features that define the major clades within Isoetes, and no fossils are known that can be definitively assigned to the crown group. While Wood et al. suggested a young origin dating to the early Cenozoic based on molecular clock estimates , the results were questioned by Wikström et al. (2023) who regarded

5460-525: The other). The repeat segments are usually between 2 bp and 10 bp but longer ones are known. Highly repetitive DNA is rare in prokaryotes but common in eukaryotes, especially those with large genomes. It is sometimes called satellite DNA . Most of the highly repetitive DNA is found in centromeres and telomeres (see above) and most of it is functional although some might be redundant. The other significant fraction resides in short tandem repeats (STRs; also called microsatellites ) consisting of short stretches of

5544-509: The parts of a gene that are transcribed into the precursor RNA sequence, but ultimately removed by RNA splicing during the processing to mature RNA. Introns are found in both types of genes: protein-coding genes and noncoding genes. They are present in prokaryotes but they are much more common in eukaryotic genomes. Group I and group II introns take up only a small percentage of the genome when they are present. Spliceosomal introns (see Figure) are only found in eukaryotes and they can represent

5628-430: The plant grew, leaving only a small cluster of leaves at the top. The lycopsids had distinctive features such as Lepidodendron lycophytes, which were marked with diamond-shaped scars where they once had leaves. Quillworts (order Isoetales) and Selaginella are considered their closest extant relatives and share some unusual features with these fossil lycopods, including the development of both bark, cambium and wood ,

5712-489: The possession of microphylls and by their sporangia, which are lateral as opposed to terminal and which open (dehisce) transversely rather than longitudinally. In some groups, the sporangia are borne on sporophylls that are clustered into strobili. Phylogenetic analysis shows the group branching off at the base of the evolution of vascular plants and they have a long evolutionary history. Fossils are abundant worldwide, especially in coal deposits . Fossils that can be ascribed to

5796-517: The possibility that they drew down enough carbon dioxide to change the Earth's climate significantly. During the Carboniferous , tree-like plants (such as Lepidodendron , Sigillaria , and other extinct genera of the order Lepidodendrales ) formed huge forests that dominated the landscape. Unlike modern trees, leaves grew out of the entire surface of the trunk and branches, but fell off as

5880-625: The primary way by which species are identified, although no one functional purpose of the intricate surface patterns is agreed upon. The megasporangia occur within the outermost microphylls (single-veined leaves) of the plant while the microsporangia are found in the innermost microphylls. This pattern of development is hypothesized to improve the dispersal of the heavier megaspore. These spores then germinate and divide into mega- and micro- gametophytes. The microgametophytes have antheridia, which in turn produce sperm. The megagametophytes have archegonia, which produce egg cells. Fertilization takes place when

5964-442: The repetitive DNA seen in other eukaryotes has been deleted from the bladderwort genome since that lineage split from those of other plants. About 59% of the bladderwort genome consists of transposon-related sequences but since the genome is so much smaller than other genomes, this represents a considerable reduction in the amount of this DNA. The authors of the original 2013 article note that claims of additional functional elements in

6048-420: The replication origin. The main features of replication origins are sequences where specific initiation proteins are bound. A typical replication origin covers about 100-200 base pairs of DNA. Prokaryotes have one origin of replication per chromosome or plasmid but there are usually multiple origins in eukaryotic chromosomes. The human genome contains about 100,000 origins of replication representing about 0.3% of

6132-500: The rest of the Lycopodiopsida class, Isoetes reproduces with spores. Among the lycophytes, both Isoetes and the Selaginellaceae (spikemosses) are heterosporous , while the remaining lycophyte family Lycopodiaceae (clubmosses) is homosporous . As heterosporous plants, fertile Isoetes sporophytes produce megaspores and microspores, which develop in the megasporangia and microsporangia. These spores are highly ornate and are

6216-552: The same glomalean phenotypes as nearby Huperzia hypogeae sporophytes. Fungal endophytes have been found in many species of lycophyte, however the function of these endophytes in host plant biology is not known. Endophytes of other plant taxa perform roles such as improving plant competitive fitness, conferring biotic and abiotic stress tolerance, promoting plant growth through phytohormone production or production of limiting nutrients. However, some endophytic fungi in lycophytes do produce medically relevant compounds. Shiraia sp Slf14

6300-422: The sides of the stems at the bases of the leaves. Although living species are small, during the Carboniferous , extinct tree-like forms ( Lepidodendrales ) formed huge forests that dominated the landscape and contributed to coal deposits. The nomenclature and classification of plants with microphylls varies substantially among authors. A consensus classification for extant (living) species was produced in 2016 by

6384-416: The spore) just enough to allow the passage of gametes. This is fundamentally different from ferns, where the gametophyte is a photosynthetic plant exposed to the elements of its environment. However, containment creates a separate problem for Isoetes, which is that the gametophytes have no way to acquire energy on their own. Isoetes sporophytes solve this problem by provisioning starches and other nutrients to

6468-480: The spores as an energy reserve for the eventual gametophytes. Although not a homologous process, this provisioning is somewhat analogous to other modes of offspring resource investment in seed-plants, such as fruits and seeds. The extent to which resources provisioned to the megaspore also support the growth of the new sporophyte is unknown in Isoetes . Spore dispersal occurs primarily in water ( hydrochory ) but may also occur via adherence to animals ( zoochory ) and as

6552-478: The summer. The quillworts are spore-producing plants and highly reliant on water dispersion. Quillworts have different ways to spread their spores based on the environment. Quillwort leaves are hollow and quill-like, with a minute ligule at the base of the upper surface. arising from a central corm . The sporangia are sunk deeply in the leaf bases. Each leaf will either have many small spores or fewer large spores. Both types of leaf are found on each plant. Each leaf

6636-455: The three orders are placed in a single class, Lycopodiopsida, holding all extant lycophyte species. Older systems have used either three classes, one for each order, or two classes, recognizing the closer relationship between Isoetales and Selaginellales. In these cases, a higher ranked taxon is needed to contain the classes (see Table 1). As Table 2 shows, the names "Lycopodiopsida" and "Isoetopsida" are both ambiguous. The PPG I system divides up

6720-456: The transcription start site of the gene. Some occur within a gene and a few are located downstream of the transcription termination site. In eukaryotes, there are some regulatory sequences that are located at a considerable distance from the promoter region. These distant regulatory sequences are often called enhancers but there is no rigorous definition of enhancer that distinguishes it from other transcription factor binding sites. Introns are

6804-432: The use of CAM is considered to avoid competition with other aquatic plants for CO 2 during daytime. The first detailed quillwort genome sequence, of I. taiwanensis , showed that there were differences from CAM in terrestrial plants. CAM involves the enzyme phosphoenolpyruvate carboxylase (PEPC) and plants have two forms of the enzyme. One is normally involved in photosynthesis and the other in central metabolism. From

6888-401: Was broad agreement, supported by both molecular and morphological evidence, that the extant lycophytes fell into three groups, treated as orders in PPG I, and that these, both together and individually, are monophyletic , being related as shown in the cladogram below:   lycopodiales     Isoetales   Selaginellales The rank and name used for the taxon holding

6972-480: Was originally known as the C-value Paradox where "C" refers to the haploid genome size. The paradox was resolved with the discovery that most of the differences were due to the expansion and contraction of repetitive DNA and not the number of genes. Some researchers speculated that this repetitive DNA was mostly junk DNA . The reasons for the changes in genome size are still being worked out and this problem

7056-562: Was published in 1922 and remained a standard reference into the twenty-first century. Even after studies with cytology, scanning electron microscopy, and chromatography, species are difficult to identify and their phylogeny is disputed. Vegetative characteristics commonly used to distinguish other genera, such as leaf length, rigidity, color, or shape are variable and depend on the habitat. Most classification systems for Isoetes rely on spore characteristics, which make species identification nearly impossible without microscopy. Some botanists split

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