Supplementary material for Karlin et al. (1999) Proc. Natl. Acad. Sci. USA 96(16), 9190-9195.
Fig. 3. Average d* differences between prokaryotic and mitochondrial DNA sequence samples based on comparisons of 50-kb samples. A representative collection of mitochondrial genomes is compared to a representative set of prokaryotes, each at least »100 kb of nonredundant DNA. A list of species follows.
Mitochondrial Genomes
Deuterostomes:
homsa (human, Homo sapiens), bosta (bovine, Bos taurus), felca (cat, Felis catus), musmu (mouse, Mus musculus), balmu (whale, Balaenoptera musculus), galga (chicken, Gallus gallus), xenla (frog, Xenopus laevis), oncmy (trout, Oncorhynchus mykiss), astpe (starfish, Asterina pectinifera), strpu (sea urchin, Strongylocentrotus purpuratus), arbli (black urchin, Arbacia lixula). Protostomes: locmi (locust, Locusta migratoria), droya (fruit fly, Drosophila yakuba), anoga (mosquito, Anopheles gambiae), albco (land snail, Albinaria coerulea), kattu (black chiton, Katharina tunicata), cepne (wood snail, Cepaea nemoralis), artfr (shrimp, Artemia franciscana), lumte (common earthworm, Lumbricus terrestris). Nematode: caeel (Caenorhabditis elegans). Fungi: schpo (fission yeast, Schizosaccharomyces pombe), allma (Allomyces macrogynus), podan (Podospora anserina). Plants: arath (Arabidopsis thaliana), marpo (liverwort, Marchantia polymorpha). Green algae: chlre (Chlamydomonas reinhardtii), prowi (Prototheca wickerhamii). Red algae: chocr (carragheen, Chondrus crispus). Protozoa: recam (Reclinomonas americana), acaca (amoeba, Acanthamoeba castellanii), parau (Paramecium aurelia), trybr (kinetoplast Trypanosoma brucei), leita (kinetoplast Leishmania tarentolae).Prokaryotic Genomes
Proteobacteria:
escco (Escherichia coli), salty (Salmonella typhimurium), klepn (Klebsiella pneumoniae), yeren (Yersinia enterocolitica), yerpe (Yersinia pestis), serma (Serratia marcescens), vibch (Vibrio cholerae), haein (Haemophilus influenzae), coxbu (Coxiella burnetii), bucap (Buchnera aphidicola), psefl (Pseudomonas fluorescens), psepu (Pseudomonas putida), pseae (Pseudomonas aeruginosa), azovi (Azotobacter vinelandii), borpe (Bordetella pertussis), alceu (Alcaligenes eutrophus), neigo (Neisseria gonorrhoeae), neime (Neisseria meningitidis), agrtu (Agrobacterium tumefaciens), rhile (Rhizobium leguminosarum), rhime (Rhizobium meliloti), braja (Bradyrhizobium japonicum), rhoca (Rhodobacter capsulatus), rhosp (Rhodobacter sphaeroides), parde (Paracoccus denitrificans), rhoru (Rhodospirillum rubrum), ricpr (Rickettsia prowazekii), myxxa (Myxococcus xanthus), helpy (Helicobacter pylori), camje (Campylobacter jejuni). Gram+: bacsu (Bacillus subtilis), bacth (Bacillus thuringiensis), staau (Staphylococcus aureus), lacla (Lactococcus lactis), strpn (Streptococcus pneumoniae), strmu (Streptococcus mutans), strpy (Streptococcus pyogenes), entfa (Enterococcus faecalis), cloac (Clostridium acetobutylicum), clobo (Clostridium botulinum), bacst (Bacillus stearothermophilus), strco (Streptomyces coelicolor), strgr (Streptomyces griseus), strhy (Streptomyces hygroscopicus), sacer (Saccharopolyspora erythraea), mycle (Mycobacterium leprae), myctu (Mycobacterium tuberculosis), corgl (Corynebacterium glutamicum). Mycoplasma: mycge (Mycoplasma genitalium), mycpn (Mycoplasma pneumoniae). Cyanobacteria: synsp (Synechococcus sp.), anasp (Anabaena sp.), synsq (Synechocystis sp.). Spirochaetes: trepa (Treponema pallidum), borbu (Borrelia burgdorferi). Other eubacteria: deira (Deinococcus radiodurans), porgi (Porphyromonas gingivalis), chltr (Chlamydia trachomatis), chlpn (Chlamydia pneumoniae), thesp (Thermus aquaticus + thermophilus), aquae (Aquifex aeolicus). Archaea: halha (Halobacterium halobium), halsa (Halobacterium salinarium), metja (Methanococcus jannaschii), metth (Methanobacterium thermoautotrophicum), arcfu (Archaeoglobus fulgidus), pyrho (Pyrococcus horikoshii), pyrae (Pyrobaculum aerophilum), sulac (Sulfolobus acidocaldarius), sulso (Sulfolobus solfataricus).