Figure 1: Genome sizes of different organisms.

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1 How big are genomes? Genomes are now being sequenced at such a rapid rate that it is fair to say that it is becoming routine. As a result, there is a growing interest in trying to understand the meaning of the information that is encoded and stored in these genomes and to understand their differences and what they say about the evolution of life on Earth. Further, it is now even becoming possible to compare the genomes between different individuals of the same species which serves as a starting point for understanding the genetic contributions to variability. Naively, the first question one might ask in trying to take stock of the information content of genomes would be how large are they? Early thinking held that the genome size should be directly related to the meaningful information content in the genome. This was strikingly refuted by the similarity in the number of protein coding genes in genomes of very different sizes, one of the unexpected results of the accumulated weight of sequencing a number of different genomes from organisms far and wide. For example, Arabidopsis thaliana (a mustard plant), Caenorhabditis elegans (a nematode) and Drosophila melanogaster (a fruit fly) all have a very similar number of protein coding genes to that of human or mouse ( 20,000) even though their genomes vary in size by over 20 fold. As shown in Figure 1, the range of genome sizes runs from roughly the 0.5 Mbp of Mycoplasma genitalium to 670 Gbp for the enormous genome of Polychaos dubium (formerly Amoeba dubia), revealing more than a million-fold difference in genome size even for different microscopic organisms. Of course, viral genomes are another matter and their sizes are considerably smaller with many of the most feared RNA viruses having genomes that are less than 10 kb in length. Converting the length in base pairs to physical length if the DNA was linearly stretched can be done by noting that the distance between bases along the DNA strand is 0.3 nm (BNID ). For the human genome totaling 3Gbp, this results in about one meter. So in each of our body s cells one has to compress this one meter into a few micrometers, the size of the nucleus. Achieving this requires packing proteins such as histones and much dexterity in reading the stored information during transcription.

2 Figure 1 gives some examples of different genome sizes with the ambition of illustrating some of the useful and well known model organisms, some of the key outliers characterized by genomes that are either extraordinarily small or large and examples which are particularly exotic. One often finds contrasting values for genome sizes even for many of the model organisms that are already sequenced. The human genome can be quoted as consisting of 2.9 Gbp or 3.2 Gbp depending on the resource that is consulted. The reason for this uncertainty can be related to the methods of measurement, sequencing usually captures only the euchromatic regions whereas the repetitive regions consisting of the heterochromatin are still often not resolved when using sequencing methods. Older methods of measuring DNA in bulk refer to the genome size through the C-value, representing the amount of DNA and thus genome length without regard to its specific sequence. This difference in what is being measured leads to contrasting values even for the most highly studied genomes. Given the large range of genome sizes revealed in Figure 1, the next vignette now takes up the question of how many genes are present in these various genomes and whether there are any useful rules of thumb for predicting the gene number on the basis of genome size. Figure 1: Genome sizes of different organisms.

3 Table 1 Genomic census for a variety of selected organisms. The table features the genome size, current best estimate for number of protein coding genes and number of chromosomes. Notice how the number of genes in bacteria and archea is similar to the size of the genome in kbp reflecting the goodness of a simple estimate that each gene is coded by roughly 1000 bp and that the majority of the genome in these cases is devoted to protein coding. Genomes often also include extra-chromosomal elements such as plasmids that might not be indicated in the genome size and number of chromosomes. The number of genes is constantly under revision. The numbers given here reflect the number of protein coding genes. trna and non coding RNAs, many of them still to be discovered, are not accounted for. Bacterial strains often show significant variations in genome size and number of genes among strains. Organism Genome size (bp) Number of genes - Protein coding (total) Number of chromosomes Model Organisms Escherichia coli 4.6 Mbp , Budding yeast Saccharomyces cerevisiae Fission yeast Schizosaccharomyces pombe Amoeba Dictyostelium discoideum Diatom Thalassiosira pseudonana Bread mold Neurospora crassa Nematode Caenorhabditis elegans Fruit fly Drosophila melanogaster Thale cress Arabidopsis thaliana (4, ) 12.1 Mbp , (6, ) ~13 Mbp , ~34 Mbp ~12, Mbp , chloroplast +40 mitochondrial genes Mbp , RNA genes Mbp , Mbp Euchromatic Original estimate ~125 Mbp Measured by flow cytometry ~157 Mbp (22, ) (n) autosomal 5 (n) , (2n) , (27, ) 10 (2n) Moss Physcomitrella 511 Mbp patens Zebrafish Danio rerio 1.2 Gbp , Mouse Mus musculus Euchromatic ~2.5 20, (2n)

4 Human Homo sapiens Gbp Total 2.64 Gbp Euchromatic 2.88 Gbp Overall 3.08 Gbp , ; 19, (Mapped genes 22, ) 46 (2n) Viruses Viroids (nonencapsulated Kb plant RNA parasites) Hepatitis d virus 1.7 Kb (smallest known RNA virus) HIV Kbp ssrna (2n) Influenza A 13.5 Kbp ssrna Bacteriophage λ 48.5 Kbp ORFs dsdna Epstein-Barr virus ~172 Kbp Acanthamoeba polyphaga Mimivirus (Largest known viral 1.18 Mbp Organelles Mitochondria - human 16.7 Kbp (37) Mitochondria - yeast 85.8 Kbp Chloroplast Kbp Arabidopsis Bacteria Carsonella ruddii (Smallest genome of an endosymbiont bacteria) Mycoplasma genitalium (smallest genome of a free living Kbp ~580 Kbp

5 bacteria) Buchnera sp Heliobacter pylori 1.67 Mbp , Haemophilus influenza (first free-living 1.83 Mbp organism sequenced) Cyanobacteria Synechococcus elongatus Methicillin resistant Staphylococcus aureus (MRSA) 2.8 Mbp , (3,041) and 2 plasmids Mbp , on plasmids and 3 plasmids Deinococcus radiodurans ~3.3 Mbp , chromosomes and 2 plasmids Caulobacter crescentus 4.02 Mbp , Bacillus subtilis ~4.2 Mbp , Sorangium cellulosum (Largest known bacterial Archaea Nanoarchaeum equitans (smallest parasitic archaeal Thermoplasma acidophilum (flourish in ph<1) Methanocaldococcus (Methanococcus) jannaschii (from ocean bottom hydrothermal vents; pressure >200 atm) 13 Mbp ~490 Kbp Mbp , (1, ) 1.66 Mbp ,682 (+ 56 on plasmids ) Pyrococcus horikoshii ~1.7 Mbp , Pyrococcus furiosus (optimum temp 100⁰C) Mbp , and 2 plasmids

6 Eukaryotes - unicellular Microsporidian Encephalitozoon cuniculi (smallest eukaryotic nuclear Ostreococcus tauri (smallest free living eukaryote) Plasmodium falciparum (chief cause of Malaria parasite) Polychaos dubium (Largest known genome size) 2.9 Mbp , Mbp , Mbp , Gbp (with many copies) Eukaryotes - multicellular Placozoan Trichoplax adhaerens Pufferfish Fugu rubripes (Smallest known vertebrate Populus trichocarpa (first tree to have its genome sequenced) Sea urchin Strongylocentrotus purpuratus 98 Mbp , (2n) Mbp Mbp Mbp ~23, Corn Zea mays 2.4 Gbp Estimated number of genes 42,000-56, (2n) Dog Canis familiaris 2.4 Gbp , (2n) Chimpanzee Pan 3.7 Gbp (2n) troglodytes Wheat Triticum 16.8 Gbp estimations range 42 (2n=6x)

7 aestivum 107, , Fritillaria assyrica Gbp (largest known plant [calculated from C value] Marbled lungfish Protopterus aethiopicus (largest known animal 130 Gbp [calculated from C value]