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Which organism has the smallest genome length?

Which organism has the smallest genome length?


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Which animal/plant/anything has smallest length genome?


Since you said plant/animal/anything, I offer the smallest genomes in various categories…

(Kb means Kilobases, Mb means Megabases. 1 Kb = 1000 base pairs, 1Mb = 1000Kb)

  • Smallest plant genome: Genlisea margaretae at 63Mb (Greilhuber et al., 2006)
  • Smallest animal genome: Pratylenchus coffeae (nematode worm) at 20Mb (Animal Genome Size DB)
  • Smallest vertebrate genome: Tetraodon nigroviridis (pufferfish) at 385Mb (Jailon et al., 2004)
  • Smallest eukaryote: Encephalitozoon cuniculi (microsporidian) at 2.9Mb (Vivarès & Méténier, 2004)
  • Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003)
  • Smallest bacterial genome: Carsonella ruddii (endosymbiont) at 160Kb (Nakabachi et al., 2006)
  • Smallest genome of anything: Circovirus at 1.8Kb (only 2 proteins!!) (Chen et al., 2003)

Refs…


I want to say Mycoplasma genitalium with a genome size of 582,970 bp. Turns out the answer is Nanoarchaeum eqitans with a genome of 490,885 bp.

http://en.wikipedia.org/wiki/Nanoarchaeum

http://www.ncbi.nlm.nih.gov/pubmed/14566062


Both Mycoplasma genitalium and Nanoarchaeum equitans are obligate parasites / endosymbionts. This means that they depend heavily on their host to support their vital functions and they have lost many of their own genes.

A really free-living organism with an extremely small genome (~1309 kbp, 1354 genes) is the heterotrophic marine alpha-proteobacterium Pelagibacter ubique [1].

See a larger analysis here: https://alamot.github.io/smallest_genome/

[1]: https://www.ncbi.nlm.nih.gov/pubmed/16109880 Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005). "Genome streamlining in a cosmopolitan oceanic bacterium". Science 309: 1242-1245.


Smallest free-living bacterial genome: Nanoarchaeum eqitans at 491Kb (Waters et al., 2003) I downloaded this paper it says that this is archaea and its obligate symbiont not a free living bacteria. Please read carefully and then upload it.


The Smallest Genome: What's the Minimum DNA Amount for Life?

The human body functions based on the activity of about 35,000 genes, comprised in 3 billion DNA bases. And even the bacteria needs hundreds of genes to cope with their metabolic functions. But there must be an extreme of functioning genes into an organism at which life is possible.

German researchers discovered in 2002, in northern Iceland, a very odd microbe inhabiting the volcanic bed of the sea. These bacteria reproduce only in very hot, oxygen free and sulfur rich waters of hydrothermal vents (associated with submarine volcanoes). Its name, Nanoarchaeum equitans ("primitive dwarf rider") refers to the fact that these types of ancient bacteria live on a much larger archebacterium (an ancient type of bacteria) called Ignicoccuis ("fire ball"), on which it depends for its growth in an obligatory symbiosis.

The microbes are so small (400 nanometers), that 6 millions would fit in a needle top. Only nanobacteria and nanobes are smaller, but many doubt their living status.

Nanoarchaeum possesses the smallest genome in the world: just 490,885 pairs of nucleotid bases. Just imagine that 3 pairs encode for an aminoacid, that a protein means from about 50-100 aminoacids to hundreds, and that each gene has a large DNA stretch which controls its activity like a starter. And many portions of the DNA do not encode genes. So that you can imagine in how very few genes this organism survives!

It lacks the genes for several vital metabolic pathways, and Nanoarchaeum cannot synthesize most nucleotides, amino acids, lipids, and cofactors. This can be compatible with life because Nanoarchaeum gets them from Ignicoccus. The organism also may not be able to produce its own ATP (the energy transporting molecule). Surprisingly, in 2006 even a smaller genome was found in a tiny symbiotic bacteria living inside special cells of a small aphid-related insect, named Carsonella ruddii.

It is only one-third the size of Nanoarchaeum's genome: just 159,662 base-pairs of DNA, which encode only 182 protein-coding genes.

Aphids eat plant saps, which are rich in sugar, but lack proteins, that's why the insects rely on Carsonella to get a balanced diet. The bacteria manufacture amino acids, and share the goodies with their hosts. Carsonella live inside the insect's cells and cannot survive on their own.

Endosymbiotic bacteria live in an extremely stable world, so they need a simple set of instructions and lost many of the metabolic pathways that free-living bacteria need to survive after so many generations of living within insects.

Carsonella lives inside a psyllid insect, called Pachypsylla venusta. It is possible that in the bacteria's evolutionary past, some of its genes were inserted into the insect's genome, allowing the insect to produce some of the metabolites required by the bacteria. This way, the bacteria lost those genes.

Animal and plant cells have specialized structures inside them, called organelles, with specific functions, and some are derived from endosymbiotic bacteria incorporated into the cell, over the course of evolution. The organelles responsible for energy production, called mitochondria, are thought to have once been free-roaming bacteria that larger cells assimilated long ago, and they still have their own DNA. Perhaps, one day Carsonella's small genome will lose its identity altogether and the microbe will turn into an organelle.


Smallest multicellular organism

I’ve been searching for the smallest multicellular organism and there do not seem to be any adult creatures with fewer than a thousand cells. For some reason there seems to be no evolutionary advantage for being say an organism of two cells or three hundred cells. This seems to also hold true for colonies of cells like sponges or algae. No one seems to have an explanation for why this would be true.

The diversity among organisms on the order of a few thousand cells is immense. On the one hand we have the nematode worm C. elegans which has 959 somatic cells with a nervous system of about 300 neurons. It has muscles and a metabolic system that operates surprisingly like humans. It reproduces sexually with sperm and egg. It’s genome has 100 million base pairs encoding an estimated 17,800 genes.

On the other hand we have Trichoplax adhaerens which is a candidate for the simplest multicellular organism. It is the only species in the phylum placozoa. Trichoplax is comprised of a few thousand cells that differentiate into four types. It has no neural or muscular systems. It basically looks and acts like a large amoeba. It reproduces by binary fission or sometimes by budding although sexual reproduction may be involved like yeast. It has the smallest genome of any known animal at 50 million base pairs which is only a factor of two smaller than the nematode.

Both animals are about the same size – a few millimetres in length – and both have roughly the same number of cells but they have employed drastically different strategies for survival. So it seems that the constraint on minimum number of cells in an animal is not one of limited strategies. Perhaps is is a result of a constraint of molecular biology or cellular physiology.


Section Summary

Prokaryotes have a single loop chromosome, whereas eukaryotes have multiple, linear chromosomes surrounded by a nuclear membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule. An organism’s traits are determined in large part by the genes inherited from each parent, but also by the environment that they experience. Genes are expressed as characteristics of the organism and each characteristic may have different variants called traits that are caused by differences in the DNA sequence for a gene.

Exercises

Glossary

diploid: describes a cell, nucleus, or organism containing two sets of chromosomes (2n)

gamete: a haploid reproductive cell or sex cell (sperm or egg)

gene: the physical and functional unit of heredity a sequence of DNA that codes for a specific peptide or RNA molecule

genome: the entire genetic complement (DNA) of an organism

haploid: describes a cell, nucleus, or organism containing one set of chromosomes (n)

homologous chromosomes: chromosomes of the same length with genes in the same location diploid organisms have pairs of homologous chromosomes, and the members of each pair come from different parents

locus: the position of a gene on a chromosome


What is the Simplest Organism Known? (with picture)

Which microbe is the simplest organism depends on your definition of a living organism. If viruses, prions, satellites, nanobes, nanobacteria (non-free-living sub-bacterial organisms) are excluded, the simplest free-living organism known is Mycoplasma genitalium, with a genome of only 580,000 base pairs and 482 protein-coding genes. Mycoplasma genitalium is a tiny parasitic bacteria that lives in the digestive and genital tracts of primates.

By comparison, Carsonella ruddii, an endosymbiotic bacteria that lives in plant lice, has a genome of only 159,662 base pairs, with just 182 genes, the smallest known. However, Carsonella ruddii cannot live on its own, and like a virus, depends on the host to survive. Previously, a thermophile that lives around underwater hot springs, Nanoarchaeum equitans, was thought to be the simplest organism, with a genome 490,885 base pairs long and a size of 400 nanometers.

Mycoplasma genitalium and other "ultramicroscopic" bacteria have diameters in the ballpark of 200-300 nanometers, smaller than some large viruses. 200 nm is about the limits of a conventional light microscope, so an electron microscope or atomic force microscope is necessary to observe these organisms. There may be free-living organisms even smaller than this — so-called nanobacteria or nanobes are around 10 - 20 nanometers in size, although their status as living organisms is controversial. No DNA has yet been successfully extracted from these objects, which may simply be mineral growths. On the other hand, among them may be the world's simplest organism.

Viruses, which cannot reproduce independently, are of course smaller and simpler than bacteria. Some of the smallest RNA viruses, retroviruses such as the Rous sarcoma virus, have genomes 3,500 base pairs in length, a diameter of about 80 nm, and only possess just four genes. The smallest DNA viruses have a smaller size (18-26 nm) but larger genomes, around 5,000 base pairs. Bacteria and viruses with tiny genomes tend to have a high ratio of protein coding genes (95-98%), in comparison to larger genomes like the human genome, where only 1.5% of genes code for proteins.

In an interesting twist on the simplest organism story, scientist Craig Venter Nobel Prize winner Hamilton Smith, working at the J. Craig Venter Institute are attempting to create an even simpler organism, Mycoplasma laboratorium, which, if successful, will also be the first example of synthetic life. Taking a Mycoplasma genitalium as a starting point, the team randomly knocks out genes and observes the resulting organism for signs of life. Venter believes that 100 of the 482 protein-coding genes in Mycoplasma are redundant, and seeks to synthesize a novel genome from scratch containing only 382 genes, then inject it into a gutted Mycoplasma genitalium, which would then reanimate, Frankenstein-style. This is called the Minimal Genome Project. The goal is to use the simplest organism to produce large amounts of hydrogen for renewable fuel.

Michael is a longtime InfoBloom contributor who specializes in topics relating to paleontology, physics, biology, astronomy, chemistry, and futurism. In addition to being an avid blogger, Michael is particularly passionate about stem cell research, regenerative medicine, and life extension therapies. He has also worked for the Methuselah Foundation, the Singularity Institute for Artificial Intelligence, and the Lifeboat Foundation.

Michael is a longtime InfoBloom contributor who specializes in topics relating to paleontology, physics, biology, astronomy, chemistry, and futurism. In addition to being an avid blogger, Michael is particularly passionate about stem cell research, regenerative medicine, and life extension therapies. He has also worked for the Methuselah Foundation, the Singularity Institute for Artificial Intelligence, and the Lifeboat Foundation.


Zebrafish, the Living Looking Glass

In the basement of the Life Sciences Building, around 1,500 fish tanks, ranging in size from briefcases to small crates, are systematically laid out in rows on metal shelves. From fertilized egg to adult, the roughly 20,000 fish represent the entire zebrafish lifecycle, providing Bruce Draper with a comprehensive view of their growth.

“If you’re looking at the process of development—so going from a fertilized egg to a swimming, feeding organism—all that process in mammals is happening in utero, so you actually have to sacrifice the mom to get the embryos out to study them,” says Draper. “With zebrafish, it’s all external fertilization.”

Part of Draper’s research focuses on problems of reproductive development. Zebrafish (Danio rerio) are well-suited for this research as their embryos are clear, providing a window into the biological machinery behind their formation. As the fish age, they develop stripes and lose their transparency.

Researchers bypass this problem by genetically modifying zebrafish with a gonad—the organ responsible for producing sperm and eggs—that glows under ultraviolet light. This allows continuous monitoring of gonad development as the fish grows, providing clues about reproductive development diseases like ovarian cancer.

Previously, Draper and his colleagues identified the gene fgf24 as important for gonad development in zebrafish. Mutant zebrafish developed defective gonads and had limited reproductive abilities. While this specific gene signaling isn’t known to be involved in mammalian gonad development, many aggressive ovarian cancers correlate with an overactive signaling pathway related to this gene. Overall, about 84 percent of the genes associated with human disease have counterparts in zebrafish.

Associate Professor Bruce Draper uses zebrafish to study gonad development. Designed by Steve Dana/UC Davis

Draper and his colleagues are investigating how single-cell RNA sequencing could help advance their research. The technique allows a high-resolution view of individual cells and the genes they express.

“We’re now identifying on a much more refined level what genes are expressed in particular cells,” he says, noting that the most aggressive forms of ovarian cancer typically occur in the organ’s cell linings. “We’re very interested in trying to identify those epithelial cells in our dataset so that we can start asking what other genes are expressed in there.”

Draper’s techniques for this project are being informed by Celina Juliano, whose office is just a few doors down from his.


6.1 The Genome

The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events in the life of a cell from the division of a single parent cell to produce two new daughter cells, to the subsequent division of those daughter cells. The mechanisms involved in the cell cycle are highly conserved across eukaryotes. Organisms as diverse as protists, plants, and animals employ similar steps.

Genomic DNA

Before discussing the steps a cell undertakes to replicate, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s complete complement of DNA is called its genome . In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle. The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth.

In eukaryotes, the genome comprises several double-stranded, linear DNA molecules (Figure 6.2) bound with proteins to form complexes called chromosomes. Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells. Human body cells (somatic cells) have 46 chromosomes. A somatic cell contains two matched sets of chromosomes, a configuration known as diploid . The letter n is used to represent a single set of chromosomes therefore a diploid organism is designated 2n. Human cells that contain one set of 23 chromosomes are called gametes , or sex cells these eggs and sperm are designated n, or haploid .

The matched pairs of chromosomes in a diploid organism are called homologous chromosomes . Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus . Genes, the functional units of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the different forms of a characteristic. For example, the shape of earlobes is a characteristic with traits of free or attached.

Each copy of the homologous pair of chromosomes originates from a different parent therefore, the copies of each of the genes themselves may not be identical. The variation of individuals within a species is caused by the specific combination of the genes inherited from both parents. For example, there are three possible gene sequences on the human chromosome that codes for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible to have two copies of the same gene sequence, one on each homologous chromosome (for example, AA, BB, or OO), or two different sequences, such as AB.

Minor variations in traits such as those for blood type, eye color, and height contribute to the natural variation found within a species. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosomes other than a small amount of homology that is necessary to reliably produce gametes, the genes found on the X and Y chromosomes are not the same.


What is a Model Organism?

When researchers look for an organism to use in their studies, they look for several traits. Among these are size, generation time, accessibility, manipulation, genetics, conservation of mechanisms, and potential economic benefit. Selected bacteria, fungi, plants or animals that can be bred and studied with simple methods and are therefore of great importance for biological and biomedical research. Model organisms are, as being used as a model, usually the first organisms of a kingdom whose entire genome was decoded. This further pushes their research capabilities.


The Tree of Life

A one page paper in Science reports on what I think is one of the most exciting findings in microbial genomics in years. The reports describes the sequencing and analysis of the genome of a bacterial endosymbiont of an aphid. This bacteria, known as Carsonella, has a TINY genome - only 160 kbp in length. This is

3 fold smaller than the previously known smallest genome - that of Nanoarchaeum equitans which has a genome of 490 kbp.

I think almost certainly this symbiont should be considered an organelle. It is missing many cellular functions found even in the most reduced symbionts. Thus in essence it may not be the smallest genome of a cellular organism. But who cares how we define it. If it is a new organelle - that is amazing. If it is a tiny cellular genome - that is amazing too.

One thing that strikes me as strange is the fact that the paper is only one page long. It contains so little detail on what was done and what was found in the genome that the story is woefully incomplete. This I would guess is somehow related to a rush to publish but also likely due to it being published in Science, which has severe page restrictions.

This paper has been getting ENORMOUS press coverage for valid reasons. But I agree with Craig Venter (see the New Scientist article) that this genome is not of much relevance to efforts to create a "minimal" genome. This is because the ideal minimal genome is one that can support independent life. Carsonella, is far from independent and thus represents a really wild evolutionary story, but nothing of much relevance to minimal genome studies.


Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H., Moran, N., & Hattori, M. (2006). The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella Science, 314 (5797), 267-267 DOI: 10.1126/science.1134196


Watch the video: Craig Venter: On the verge of creating synthetic life (May 2022).