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Gutell 023.nar.1992.20.sup.2095

  1. 1. Nucleic Acids Research, Vol. 20, Supplement 2095-2109A compilation of large subunit (23S- and 23S-like)ribosomal RNA structuresRobin R.Gutell*, Murray N.Schnare1 and Michael W.Grayl*Molecular, Cellular, and Developmental Biology, Campus Box 347, University of Colorado, Boulder,CO 80309 and 1Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7,CanadaINTRODUCTIONThe present edition of large subunit (LSU; 23S and 23S-like)rRNA secondary structures updates and refines the collectionsof 1988 [1] and 1990 [2]. As in [1] and [2], each LSU rRNAsequence is presented as a secondary structure, a two-dimiensionalformat that represents, in part, the biologically relevantconformation of the rRNA molecule. When LSU rRNAsequences are configured in this manner, valuable phylogeneticinformation is readily extracted, facilitating the identification ofconserved and variable regions. At the same time, the secondarystructure serves as an effective template for relating form tofunction.GROWTH OF THE DATABASEThe collection of LSU rRNA sequences has continued its steadyincrease in the twelve years following publication of the firstcomplete and correct 23S rRNA sequence [3]. The growth ofthis collection is tracked in Table 1, with numbers reflecting thosesequences that are in the public domain. Within the past fewyears, a small but growing number of sequences have beenreleased through the GenBank/EMBL databases prior to formalpublication; some of these entries still lack a journal citation.Those sequences new to our collection are appropriately notedin Table 2.MODELS OF HIGHER-ORDER STRUCTUREIn deducing higher-order structure, comparative analysis is usedto reveal features common to all homologous rRNAs. Thisapproach has resulted in detailed and progressively refined higher-order structures for the 23S and 16S rRNAs ofEscherichia coli,the standards to which all other homologous rRNA structuresare referred. Initially, with a minimal number of LSU rRNAsequences available for comparison, several alternative secondarystructures were proposed [4-6]. As both the number andphylogenetic diversity of LSU rRNA sequences increased, itbecame possible to test and correct existing models, taking outor adding helices and/or base pairs as appropriate. More recently,expansion ofthe sequence dataset has made it possible to identifya number of tertiary pairings. The current version of the E. coli23S rRNA secondary structure is the culmination of over tenyears of analysis [7,8]; all of the secondary structure pairingsand proposed tertiary interactions are now strongly supportedby comparative data. We anticipate, however, that additionaltertiary interactions will continue to be discovered as new LSUrRNA sequences appear.The evolutionary process has affected the size as well as theprimary structure of LSU rRNAs. The smallest such RNAs arethose found in the kinetoplast (mitochondrion) of thetrypanosomatid flagellates, such as Crithidia fasciculata (1141nt), while the largest are those in the cytoplasmic ribosomes ofvertebrates, e.g., humans (5182 nt; 5.8S + 28S). Whilecomparative analysis has defined a core of higher-order structurecommon to all LSU rRNAs, certain other structures are foundonly within particular phylogenetic subsets. Elucidation ofthesephylogenetically restricted structures requires comparison of atleast several related LSU rRNA sequences (the number dependingon the rate at which such structures are diverging).In the case of those LSU rRNAs comparable in size to E. coli23S rRNA, secondary structures have been modeled in theirentirety. Larger LSU rRNAs (eucaryotic cytoplasmic and somemitochondrial) contain apparent insertions relative to the E. colistructure. Within the past year, a number of these previouslyunstructured regions have been configured by comparativemethods. As additional LSU rRNA sequences are determined,especially within localized phylogenetic divisions, we anticipatethat each remaining unstructured region will be resolved. It isof interest that within the eucaryotic nucleocytoplasmic lineage,several of these recently structured regions are common only toa relatively narrow phylogenetic grouping.All secondary structures follow the convention and layoutestablished for the E. coli 23S rRNA model, the de factoreference structure. The majority of homologous primary andsecondary structure features are displayed in an analogousgraphical manner to emphasize this structural homology. In asmall number of cases, due to insertion/deletion events, thisgraphical representation varies somewhat for structural elementsdeemed to be homologous. In future editions of this secondarystructure compendium, we will begin to incorporate tertiaryinteractions that satisfy comparative criteria.* To whom correspondence should be addressed.=/ 1992 Oxford University Press
  2. 2. 2096 Nucleic Acids Research, Vol. 20, SupplementAVAILABILITY AND STATUS OF STRUCTUREFIGURESAs in [2], the actual 23S rRNA secondary structures are notpublished here. Instead, readers will find (i) a table of completeLSU rRNA sequences, grouped according to phylogeneticdivision and including GenBank/EMBL Accession Numbers(Table 2), and (ii) a publication reference list for these sequences.The comprehensive set of LSU rRNA secondary structures maybe obtained in one of two ways. Hardcopy printouts of thisset are available directly from us (inquiries should be referredto M.W.G. at the address listed below). Release 1.0, whichcomprises 88 structures (see Table 2), is immediately available.This release contains virtually finalized archaebacterial,eubacterial and plastid structures. Mitochondrial structures havebeen extensively revised from those first presented in [1], buta further round of (relatively minor) revision is necessary beforethese models will be in final form. Eukaryotic cytoplasmicstructures in Release 1.0 are largely unchanged from those givenin [1]; an exception is the newly modeled Euglena graciliscytoplasmic secondary structure [9], which does contain revisionsthat are being incorporated into the secondary structures ofothernucleus-encoded LSU rRNAs. Newly modeled and refined LSUrRNA secondary structures will be included in Release 2.0,hardcopies of which should be ready for distribution before theend of 1992. Inquliries about hardcopy printouts should stateexplicitly which Release (1.0 or 2.0) is being requested.Alternatively, individuals with access to the Internettelecommunications network and a laser printer capable ofprocessing PostScriptTm files may elect to obtain files of LSUrRNA secondary structures by anonymous file transfer protocol(ftp). These rdes are deposited with the Ribosomal RNADatabase Project [10] on the RDP computer at the ArgonneNational Laboratory, and may be accessed as indicated below.Inquiries concerning this on-line service may be directed toR.R.G. (e-mail and postal addresses as noted below).As time and facilities permit, the rRNA information availableon-line will be increased. Initially, it will include the completeset of LSU rRNA secondary structures (in PostScriptTm format),the table of LSU rRNA sequences and their accession numbers,and the associated publication reference list. Refinements toexisting secondary structures as well as newly modeled secondarystructures will be released on-line as soon as we have completedour own analysis. From time to time, we will also update theassociated table and reference list. Currently we include onlythose LSU rRNA sequences that are complete (or nearly so).ACCURACY OF THE DATAAmbiguous positions in a published sequence are specifiedaccording to the nomenclature recommended by IUPAC (e.g.,Y = pyrimidine ; R = purine; etc.). As noted in Table 2 andthe List of References, there are independently determinedversions ofthe same primary sequence for several LSU rRNAs.Usually, these alternative versions differ from one another at anumber of positions, and at least some of these differences arelikely to be sequencing errors. Often, the secondary structurepredicts which version of the sequence is likely to be correct ata particular position. On the other hand, it is probable that someof the variation actually reflects genuine inter- or intra-strainwithin variable regions [11]. We have also noted that a fewpublished primary sequences differ at one or more positions fromtheir GenBank/EMBL listings, without an indication that thedatabase entry represents a subsequently revised version of theoriginal published sequence. Again, secondary structure modelingmay or may not indicate which version is likely to be correct.It is our intent to provide brief annotation in the hardcopy andelectronic versions ofthe secondary structure figures to indicatewhich version ofthe primary sequence has been used at discrepantpositions.In compiling the reference list, we have checked each ofthesecitations against the original published paper. We note that citationinformation in the GenBank/EMBL database is occasionallyinaccurate, and for that reason we have provided completereferences, including titles.Finally, we invite further comments from readers, and welcomesuggested revisions/alternative interpretations to the proposedsecondary structures, as well as suggestions for improvement inthe content and/or form of the database. We also solicit newlydetermined LSU rRNA sequences in advance of publication, inorder to accelerate their inclusion in the compendium.ACKNOWLEDGMENTSWe gratefully acknowledge the computer programming expertiseof Bryn Weiser and Tom Macke in this endeavor. Work on thiscompendium by M.N.S. and M.W.G. is supported by anoperating grant (MT-1 1212) from the Medical Research Councilof Canada to M.W.G. We thank the Canadian Institute forAdvanced Research (CIAR) for providing funds in support ofthe production and distribution of secondary structure figures.M.W.G. is a Fellow and R.R.G. is an Associate in the Programin Evolutionary Biology of the CIAR. We also thank theW.M.Keck Foundation for their generous support of RNAscience on the Boulder campus.REQUESTSFor hard copies of LSU rRNA secondary structures, eitherthe complete compilation or selected portions thereof (pleasespecify Release 1.0 or 2.0):M.W. Gray,Department of Biochemistry,Sir Charles Tupper Medical Building,Dalhousie University,Halifax, Nova Scotia B3H 4H7, Canada.FAX: (902)494-1355e-mail: (via Bitnet)For information about on-line availability of LSU rRNAsecondary structure files and other information contained inthis compendium:R.R. Gutell,Molecular, Cellular, and Developmental Biology,Campus Box 347,University of Colorado,Boulder, Colorado 80309, U.S.A.FAX: (303)492-7744sequence heterogeneity, particularly if the differences occur e-mail: rgutelIC&
  3. 3. Nucleic Acids Research, Vol. 20, Supplement 2097To obtain PostScriptTM files of LSU rRNA secondarystructures via anonymous ftp on the Internettelecommunications network:ftp site: info.mcs.anl.govdirectory: /pub/RDP/Contrib/RobinGutellREFERENCES1. Gutell,R.R. and Fox,G.E. (1988) Nucleic Acids Res. 16, Supplement,r175-r269.2. Gutell,R.R., Schnare,M.N. and Gray,M.W. (1990) Nucleic Acids Res. 18,Supplement, 2319-2330.3. Brosius,J., Dull,T.J. and Noller,H.F. (1980) Proc. Natl. Acad. Sci. U.S.A.77, 201-204.4. Glotz,C., Zwieb,C., Brimacombe,R., Edwards, K. and Kossel,H. (1981)Nucleic Acids Res. 9, 3287-3306.5. Branlant,C., Krol,A., Machatt,M.A., Pouyet,J., Ebel,J.-P., Edwards,K. andKossel,H. (1981) Nucleic Acids Res. 9, 4303-4324.6. Noller,H.F., Kop,J., Wheaton,V., Brosius,J., Gutell,R.R., Kopylov,A.M.,Dohme,F., Herr,W., Stahl,D.A., Gupta,R. and Woese,C.R. (1981) NucleicAcids Res. 9, 6167-6189.7. Larsen,N. (1992) Proc. Natl. Acad. Sci. U.S.A., in press.8. Gutell,R.R., Larsen,N. and Woese,C.R. (1992) In Ribosomal RNA: Structure,Evolution, Gene Expression and Function in Protein Synthesis(Zimmermann,R.A. and Dahlberg,A.E., eds.), The Telford Press, Caldwell,N.J., in press.9. Schnare,M.N. and Gray,M.W. (1990) J. Mol. Biol. 215, 73-83.10. Olsen,G.J., Larsen,N. and Woese,C.R. (1991) Nucleic Acids Res. 19,Supplement, 2017-2021.11. Gonzalez,I.L., Gorski,J.L., Campen,T.J., Dorney,D.J., Erickson,J.M.,Sylvester,J.E. and Schmickel,R.D. (1985) Proc. Natl. Acad. Sci. U.S.A.82, 7666-7670.The present publication should be quoted as reference for secondary structuredata obtained either as hard copies from the authors or from the electronicallyaccessible compilation.
  4. 4. 2098 Nucleic Acids Research, Vol. 20, SupplementTable 1. Growth of the LSU rRNA database1988 1990 1992Archaebacterial 6 7 12Eubacterial 5 13 21Plastid 4 8 13Mitochondrial 17 27 54Eukaryotic (nuclear) 10 16 28All 42 71 128Table 2. List of complete LSU rRNA sequencesOrganism namel Status2 Accession NumberARCHAEBACTIERIA (ARCHAEA3)Euryarchaeota3Archaeoglobusfulgidus *# M64487Halobacterium halobium + X00872,X03407Halobacterium marismortui + X13738Halococcus morrhuae + X05481Methanobacterium thermoautotrophicum + X15364Methanococcus vannielii + X02729Methanospirillum hungatei * # M61738,M81323Thermoplasma acidophilumn + # M20822,M32298Crenarchaeota3Desulfurococcus mobilis + X05480Sulfolobus solfataricus * # M67495Thermofdlumpendens + # X14835Thermoproteus tenax +EUBACTERIA (BACTERIA3)Gram positive bacteria4High G+C subdivisionFrankia sp.Micrococcus luteusMycobacterium lepraeStreptomyces ambofaciensStreptomyces griseusLow G+C subdivisionBacillus sp.Bacillus stearothermophilusBacillus subtilisPurple photosynthetic bacteria and their relatives4Alpha subdivisionRhodobacter capsulatusRhodobacter sphaeroidesBeta subdivisionPseudomonas cepaciaGamma subdivisionEscherichia coliPseudomnonas aeruginosaRuminobacter amylophilus+#+#M55343X06484X56657-M27245X55435,X61478X60981+ K02663+ K00637,M10606,X00007+ X06485+ # X53853,X53854,X53855+ X16368+ J01695+ Y00432+ X06765
  5. 5. Nucleic Acids Research, Vol. 20, Supplement 2099Organism namel Status2 Accession NumberSpirochetes and their relatives4Leptospira interrogans + X14249Bacteroides, flavobacteria and cytophagas and relatives4Flavobacterium odoratum + # M32365,M62807Flexibacterflexilis + # M31904,M62806Cyanobacteria4Anacystis nidulans + X00343,X00512Green sulfur bacteria4Chlorobium limicola + # M31904,M62805Planctomyces and their relatives4Pirellula marina + X07408Radio-resistant micrococci4Thermus thermophilus + X12612PLASTIDSProtoctista5Apicomplexa6Plasmodiumfalciparum6 * # X61660Euglenophyta (euglenoid flagellates)Astasia longa + X14386Euglena gracilis + X13310Chlorophyta (unicellular green algae)Chlamydomonas eugametos *Chlamydoinonas reinhardtii + X15727,X16686,X16687Chlorella ellipsoidea + M36158PlantaeBryophytaMarchantia polymorpha (liverwort) + X01647,X04465Angiospermophyta (flowering plants)Alnus incana (alder) * # M76448,M75722,M75719Conopholis americana *# X59768Nicotiana tabacum (tobacco) + J01446,1X0044Oryza sativa (rice) + X15901Pisum sativutm (pea) + # M37430Zea mays (maize) + X01365MITOCHONDRIAProtoctista5Zoomastigina (zooflagellates)CrithidiafasciculataCrithidia oncopeltiLeishmania tarentolaeLeptomonas sp.Trypanosoma bruceiChlorophyta (unicellular green algae)Chlamydomonas reinhardtiiCiliophora (ciliates)ParameciumprimaureliaParamecium tetraureliaTetrahymenapyriformis+ X02548+# X51736+ X02354+ J03814+ X02547+ M22649,M25123-25130,X54860+ K00634+ K01749,X15917+# M58010,M58011
  6. 6. 2100 Nucleic Acids Research, Vol. 20, SupplementOrganism namel Status2 Accession NumberFungiAscomycotaAspergillus nidulansNeurospora crassaPodospora anserinaSaccharomyces cerevisiaeSchizosaccharomycespombePlantaeBryophytaMarchantia polymorpha (liverwort)Angiospermophyta (flowering plants)Oenothera berteriana (primrose)Triticum aestivum (wheat)Zea mays (maize)AnimaliaNematodaAscaris suumCaenorhabditis elegansArthropodaAedes albopictus (mosquito)Apis mellifera (honeybee)Artemia salina (brine shrimp)Drosophila melanogaster (fruit fly)Drosophila yakuba (fruit fly)Locusta migratoria (locust)SpodopterafrugiperdaEchinodermata (sea urchins)Paracentrotus lividusStrongylocentrotwspurpuratusChordataAepyceros melampusAntilocapra americanaBalaenoptera physalus (fin whale)Bos taurus (ox)Boselaphus tragocamelusCapra hircus (goat)Cephalophus maxwelliCervus unicolor (sambar deer)Cyprinus carpio (carp)Danaliscus dorcasGallus gallus domesticus (chicken)Gazella thomsoniHomo sapiens (human)Hydropotes inermis (Chinese water deer)Kobus ellipsiprymnusMadoqua kirkiMuntiacus reevesi (Reeves muntjac)Mus musculus (mouse)Odocoileus virginianus (white-tailed deer)OryxgazellaRana catesbeiana (frog)+# X06961X55443M30937,X14735J01527X06597* # M68929+ X02559+ M37274+ K01868* # X54253* # X54252+ X01078+ X05011+ M21833,X12965+ # X53506+ X03240+ X05287* # M76713+ J04815+ X12631+#+#+#+#M86496M55540X61145J01394M86494M55541M86498M35875X61010M86499X52392M86501J01415,M12548,V00710M35876M86497M86495M35877J01420M35874M86500X12841
  7. 7. Nucleic Acids Research, Vol. 20, Supplement 2101Organism namel Status2 Accession NumberRattus norvegicus (rat) + J01438Tragelaphus imberbis * # M86493Tragulus napu + # M55539Xenopus laevis (toad) + M10217EUCARYOTES (EUCARYA3) (NUCLEOCYTOPLASMIC)Archezoa7Giardia ardeaeGiardia intestinalisProtoctista5Dinoflagellata (dinoflagellates)Prorocentrum micansEuglenophyta (euglenoid flagellates)Euglena gracilisZoomastigina (zooflagellates)CrithidiafasciculataTrypanosoma bruceiCiliophora (ciliates)TetrahymenapyriformisTetrahymena thermophilaAcrasiomycota (cellular slime molds)Dictyostelium discoideumMyxomycota (plasmodial slime molds)Didymium iridisPhysaruompolycephalumFungiZygomycotaAscomycotaMucor racemosusSaccharomyces carlsbergensisSaccharomyces cerevisiaePlantaeAngiospermophyta (flowering plants)Arabidopsis thalianaCitrus limon (lemon)Fragaria ananassa (strawberry)Lycopersicon esculentum (tomato)Oryza sativa (rice)Sinapsis alba (mustard)AnimaliaNematodaCaenorhabditis elegansArthropodaDrosophila melanogasterChordataHerdrnania momusHomo sapiens (human)Mus musculus (mouse)* # X58290* # X52949* X15973,X16108+ # X53361+ Y00055* # X14553* # M10752,X54004+# X54512* X00601*# X60210+ V01159* M26190* V01285+ J01355,K01048* # X52320* X05910* # X15589,X58118* X07889,X13557+ M11585*# XX15915,X57137+ X03680+ M21017* # X53538+ J01866,M11167+ J01871,X00525
  8. 8. 2102 Nucleic Acids Research, Vol. 20, SupplementOrganism namel Status2 Accession NumberRatus norvegicus (rat) + J01881,K01591,X00521,X01069Xenopus borealis (toad) * # X59733Xenopus laevis (toad) + K01376,X00136,X59734Eucaryotic organisms are classified according to the scheme of Margulis,L. and Schwartz,K.V. (1988) [Five Kingdoms. An Illustrated Guide to thePhyla ofLife on Earth (2nd edition). W.H. Freeman and Co., New York].2New listings that did not appear in the previous edition [Gutell,R.R., Schnare,M.N. and Gray,M.W. (1990) Nucleic Acids Res. 18, Supplement,2319-2330] are denoted by #. Secondary structures now available in hardcopy form in Release 1.0 are denoted by +, while newly modeled structuresthat will be included in future releases are indicated by *.3See Woese,C.R., Kandler,O. and Wheelis,M.L. (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, andEucarya. Proc. Natl. Acad. Sci. U.S.A. 87, 4576-4579.4See Woese,C.R., Stackebrandt,E., Macke,T.J. and Fox, G.E. (1985) A phylogenetic definition of the major eubacterial taxa. System. Appl. Microbiol.6, 143-151.5The term Protoctista, as defined and used by Margulis and Schwartz (1988), includes but is not limited to the Protista (unicellular eucaryotes, orprotists).6See note in List of References, below.7See Cavalier-Smith,T. (1987) Eukaryotes with no mitochondria. Nature 326, 332-333.List of references to LSU rRNA sequences (# = new this edition)ARCHAEBACTERIAArchaeoglobus fulgidus#Woese,C.R., Achenbach,L., Rouviere,P. and Mandelco,L. (1991) System. Appl. Microbiol. 14, 364-371.Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts.Desulfurococcus mobilisLeffers,H., Kjems,J., Ostergaard,L., Larsen,N. and Garrett,R.A. (1987) J. Mol. Biol. 195, 43-61.Evolutionary relationships amongst archaebacteria. A comparative study of23 S ribosomal RNAs of a sulpur-dependent extreme thermophile, an extremehalophile and a thermophilic methanogen.Halobactenum halobiumMankin,A.S. and Kagramanova,V.K. (1986) Mol. Gen. Genet. 202, 152-161.Complete nucleotide sequence of the single ribosomal RNA operon of Halobacterium halobium: secondary structure of the archaebacterial 23S rRNA.Halobactenum mwismofluBrombach,M., Specht,T., Erdmann,V.A. and Ulbrich,N. (1989) Nucleic Acids Res. 17, 3293.Complete nucleotide sequence of a 23S ribosomal RNA gene from Halobacterium marismortui.Halococcus morrhuae (see Desulfurococcus mobilis)Methanobactenum thermoautotrophicum (see Desulfurococcus mobilis)Methanococcus vannielfiJarsch,M. and Bock,A. (1985) Mol. Gen. Genet. 200, 305-312.Sequence of the 23S rRNA gene from the archaebacterium Methanococcus vannielii: evolutionary and functional implications.Methanospirillum hungatei#Burggraf,S., Ching,A., Stetter,K.O. and Woese,C.R. (1991) System. Appl. Microbiol. 14, 358-363.The sequence of Methanospirillum hungatei 23S rRNA confirms the specific relationship between the extreme halophiles and the Methanomicrobiales.Sulfolobus solfatwicus#Woese,C.R. Unpublished.Thermofilum pendens#Kjems,J., Leffers,H., Olesen,T., Holz,I. and Garrett,R.A. (1990) System. Appl. Microbiol. 13, 117-127.Sequence, organization and transcription of the ribosomal RNA operon and the downstream tRNA and protein genes in the archaebacterium 7hermofilumpendens.Thermoplasma acidophilum#Ree,H.K. and Zimmermann,R.A. (1990) Nucleic Acids Res. 18, 4471-4478.Organization and expression of the 16S, 23S and 5S ribosomal RNA genes from the archaebacterium Thermoplasma acidophilum.Thermoproteus tenaxKjems,J., Leffers,H., Garrett,R.A., Wich,G., Leinfelder,W. and B6ck A. (1987) Nucleic Acids Res. 15, 4821-4835.Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archaebacterium 7hermoproteus tenax.EUBACTERIAAnacystis nidulansKumano,M., Tomioka,N. and Sugiura,M. (1983) Gene 24, 219-225.The complete nucleotide sequence of a 23S rRNA gene from a blue-green alga, Anacystis nidulans.Douglas,S.E. and Doolittle,W.F. (1984) Nucleic Acids Res. 12, 3373-3386.Complete nucleotide sequence of the 23S rRNA gene of the Cyanobacterium, Anacystis nidulans.
  9. 9. Nucleic Acids Research, Vol. 20, Supplement 2103BaciUlus sp.# Fink,P.S., Zhao,Y., Prochaska,L.J. and Leffak,M. (1991) Nucleic Acids Res. 19, 5437.Nucleotide sequence of a 23S and a 5S-like rRNA gene from the thermophilic Bacillus sp.strain PS3.BaciUus stearothermophilusKop,J., Wheaton,V., Gupta,R., Woese,C.R. and Noller,H.F. (1984) DNA 3, 347-357.Complete nucleotide sequence of a 23S ribosomal RNA gene from Bacillus stearothermophilus.Bacilus subtilisGreen,C.J., Stewart,G.C., Hollis,M.A., Vold,B.S. and Bott,K.F. (1985) Gene 37, 261-266.Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB.Chlorobium linicola#Woese,C.R., Mandelco,L., Yang,D., Gherna,R. and Madigan,M.T. (1990) System. Appl. Microbiol. 13, 258-262.The case for relationship of the Flavobacteria and their relatives to the green sulfur bacteria.Escherichia coliBrosius,J., Dull,T.J. and Noller,H.F. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 201-204.Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli.Branlant,C., Krol,A., Machatt,M.A., Pouyet,J., Ebel,J.-P., Edwards,K. and Kossel,H. (1981) Nucleic Acids Res. 9, 4303-4324.Primary and secondary structures ofEscherichia coli MRE 600 23S ribosomal RNA. Comparison with models ofsecondary structure for maize chloroplast23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs.Flavobactenum odoratum (see Chlorobum limicola)Flexibterflexilis (see Chlorobium limicola)Franlda sp.# Normand,P. Unpublished.Leptospira interrogansFukunaga,M., Horie,I. and Mifuchi,I. (1989) Nucleic Acids Res. 17, 2123.Nucleotide sequence of a 23S ribosomal RNA gene from Leptospira interrogans serovar canicola strain Moulton.Micrococcus luteusRegensburger,A., Ludwig,W., Frank,R., Blocker,H. and Schleifer,K.H. (1988) Nucleic Acids Res. 16, 2344.Complete nucleotide sequence of a 23S ribosomal RNA gene from Micrococcus luteus.Mycobacterium leprae#Liesack,W., Sela,S., Bercovier,H., Pitulle,C. and Stackebrandt,E. (1991) FEBS Leu. 281, 114-118.Complete nucleotide sequence of the Mycobacterium leprae 23 S and 5 S rRNA genes plus flanking regions and their potential in designing diagnosticoligonucleotide probes.Pireflula mannaLiesack,W., Hopfl,P. and Stackebrandt,E. (1988) Nucleic Acids Res. 16, 5194.Complete nucleotide sequence of a 23S ribosomal RNA gene from Pirellula marina.Pseudomonas aeruginosaToschka,H.Y., Hopfl,P., Ludwig,W., Schleifer,K.H., Ulbrich,N. and Erdmann,V.A. (1987) Nucleic Acids Res. 15, 7182.Complete nucleotide sequence of a 23S ribosomal RNA gene from Pseudomonas aeruginosa.Pseudomonas cepaciaHopfl,P., Ludwig,W., Schleifer,K.H. and Larsen,N. (1989) Eur. J. Biochem. 185, 355-364.The 23S ribosomal RNA higher-order structure of Pseudomonas cepacia and other prokaryotes.Rhodobacter capsulatusHopfl,P., Ludwig,W. and Schleifer,K.H. (1988) Nucleic Acids Res. 16, 2343.Complete nucleotide sequence of a 23S ribosomal RNA gene from Rhodobacter capsulatus.Rhodobacter sphaeroides# Dryden,S.C. and Kaplan,S. (1990) Nucleic Acids Res. 18, 7267-7277.Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides.Ruminobacter amylophilusSpiegl,H., Ludwig,W., Schleifer,K.H. and Stackebrandt,E. (1988) Nucleic Acids Res. 16, 2345.Complete nucleotide sequence of a 23S ribosomal RNA gene from Ruminobacter amylophilus.Streptomyces ambofaciensPemodet,J.-L., Boccard,F., Alegre,M.-T., Gagnat,J. and Gudrineau,M. (1989) Gene 79, 33-46.Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens.Streptomyces griseus# Kim,E. Unpublished.Thermus thermophilusHopfl,P., Ulrich,N., Hartmann,R.K., Ludwig,W. and Schleifer,K.H. (1988) Nucleic Acids Res. 16, 9043.Complete nucleotide sequence of a 23S ribosomal RNA gene from 7hermus thermophilus HB8.PLASTIlSAlnus incana# Levesque,M. and Johnson,D.A. Unpublished.Sequence of the chloroplast 23S rRNA gene from the alder Alnus incana.Astasia longa#Siemeister,G. and Hachtel,W. (1990) Curr. Genet. 17, 433-438.Organization and nucleotide sequence of ribosomal RNA genes on a circular 73 kbp DNA from the colourless flagellate, Astasia longa.
  10. 10. 2104 Nucleic Acids Research, Vol. 20, SupplementChiamydomonas eugametos#Turmel,M., Boulanger,J., Schnare,M.N., Gray,M.W. and Lemieux,C. (1991) J. Mol. Biol. 218, 293-311.Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlimydomonas eugametos.Chlamydomonas reinhardtiiLemieux,C., Boulanger,J., Otis,C, and Turmel,M. (1989) Nucleic Acids Res. 17, 7997.Nucleotide sequence of the chloroplast large subunit rRNA gene from Chlamydomonas reinhardtii.ChloreUla elipsoideaYamada,T. and Shimaji,M. (1987) Curr. Genet. 11, 347-352.An intron in the 23S rRNA gene of the Chlorella chloroplasts: Complete nucleotide sequence of the 23S rRNA gene.Conopholis amencana.#Wimpee,C.F., Morgan,R. and Wrobel,R. (1992) Plant Mol. Biol. 18, 275-285.An aberrant plastid ribosomal RNA gene cluster in the root parasite Conopholis americana.Euglena gracilisYepiz-Plascencia,G.M., Jenkins,M.E. and Hallick,R.B. (1988) Nucleic Acids Res. 16, 9340.Nucleotide sequence of the Euglena gracilis chloroplast 23S rRNA gene of the rrnC operon.#Schnare,M.N., Yepiz-Plascencia,G.M., Copertino,D.W., Hallick,R.B. and Gray,M.W. (1992) Nucleic Acids Res. 20, in press.5- and 3-terminal sequences of the chloroplast 16S and 23S ribosomal RNAs of Euglena gracilis.Marchania polymorphaOhyama,K., Fukuzawa,H., Kohchi,T., Shirai,H., Sano,T., Sano,S., Umesono,K., Shiki,Y., Takeuchi,M., Chang,Z., Aota,S., Inokuchi,H. and Ozeki,H.(1986) Plant Mol. Bio. Reporter 4, 148-175.Complete nucleotide sequence of liverwort Marchantia polymorpha chloroplast DNA.[See also: Nature 322, 572-574 (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplastDNA.]Kohchi,T., Shirai,H., Fukuzawa,H., Sano,T., Komano,T., Umesono,K., Inokuchi,H., Ozeki,H. and Ohyama,K. (1988) J. Mol. Biol. 203, 353-372.Structure and organization of Marchantia polymorpha chloroplast genome. IV. Inverted repeat and small single copy regions.Nicotiana tabacumTakaiwa,F. and Sugiura,M. (1982) Eur. J. Biochem. 124, 13-19.The complete nucleotide sequence of a 23-S rRNA gene from tobacco chloroplasts.Shinozaki,K., Ohme,M., Tanaka,M., Wakasugi,T., Hayashida,N., Matsubayashi,T., Zaita,N., Chunwongse,J., Obokata,J., Yamaguchi-Shinozaki,K.,Ohto,C., Torazawa,K., Meng,B.Y., Sugita,M., Deno,H., Kamogashira,T., Yamada,K., Kusuda,J., Takaiwa,F., Kato,A., Tohdoh,N., Shimada,H.and Sugiura,M. (1986) Plant Mol. Biol. Reporter 4, 111-147.The complete nucleotide sequence of the tobacco chloroplast genome.[See also: EMBO J. 5, 2043 -2049 (1986). The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression.]Oryza saivaHiratsuka,J., Shimada,H., Whittier,R., Ishibashi,T., Sakamoto,M., Mori,M., Kondo,C., Honji,Y., Sun,C.-R., Meng,B.-Y., Li,Y.-Q., Kanno,A.,Nishizawa,Y., Hirai,A., Shinozaki,K.and Sugiura,M. (1989) Mol. Gen. Genet. 217, 185-194.The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a majorplastid DNA inversion during the evolution of the cereals.Pisum sativum#Stumnmann,B.M., Lehmbeck,J., Bookjans,G. and Henningsen,K.W. (1988) Physiologia Plantarum 72, 139-146.Nucleotide sequence of the single ribosomal RNA operon of pea chloroplast DNA.Plasmodium faldiparum#Wilson,R.J.M., Gardner,M.J., Feagin,J.E., Moore,D., Rangachari,K. and Williamson,D.H. Unpublished.A large subunit ribosomal RNA gene from the inverted repeat within the 35-kb circular DNA of the malaria parasite Plasmodium falciparum.[Note that preliminary phylogenetic analysis suggests that the P. falciparum 35-kbp DNA may be a plastid DNA remnant; see #Gardner,M.J., Feagin,J.E.,Moore,D.J., Spencer,D.F., Gray,M.W., Williamson,D.H. and Wilson,R.J.M. (1991) Mol. Biochem. Parasitol. 48, 77-88.]Zea maysEdwards,K. and Kossel,H. (1981) Nucleic Acids Res. 9, 2853-2869.The rRNA operon from Zea mays chloroplasts: nucleotide sequence of 23S rDNA and its homology with E. coli 23S rDNA.MITOCHONDRIAAedes albopictusHsuChen,C.-C., Kotin,R.M. and Dubin,D.T. (1984) Nucleic Acids Res. 12, 7771-7785.Sequences of the coding and flanking regions of the large ribosomal subunit RNA gene of mosquito mitochondria.Aepyceros melampus#Allard,M.W., Miyamoto,M.M., Jarecki,L., Kraus,F. and Tennant,M.R. (1992) Proc. Natl. Acad. Sci. U.S.A., in press.DNA Systematics and evolution of the artiodactyl family Bovidae.Antlocapra amencana#Kraus,F. and Miyamoto,M.M.(1991) Syst. Zool. 40, 117-130.Rapid cladogenesis among the pecoran ruminants: Evidence from mitochondrial DNA sequences.Apis mellferaVlasak,I., Burgschwaiger,S. and Kreil,G. (1987) Nucleic Acids Res. 15, 2388.Nucleotide sequence of the large ribosomal RNA of honeybee mitochondria.Ariemia saUnaPalmero,I., Renart,J. and Sastre,L. (1988) Gene 68, 239-248.Isolation of cDNA clones coding for mitochondrial 16S ribosomal RNA from the crustacean Artemia.
  11. 11. Nucleic Acids Research, Vol. 20, Supplement 2105Ascaris suum#Okimoto,R., Macfarlane,J.L., Clary,D.O. and Wolsteholme,D.R. (1992) Genetics, in press.The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.AspergiUus nidulansNetzker,R., Kochel,H.G., Basak,N. and Kuntzel,H. (1982) Nucleic Acids Res. 10, 4783-4794.Nucleotide sequence ofAspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins,four tRNAs and L-rRNA.Dyson,N.J., Brown,T.A., Waring,R.B. and Davies R.W. (1989) Gene 75,109-118.The mitochondrial ribosomal RNA molecules of Aspergillus nidulans.Balaenoptera physalus#Arnason,U., Gullberg,A. and Widegren,B. (1991) J. Mol. Evol. 33, 556-568.The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus.Bos taurusAnderson,S., de Bruijn,M.H.L., Coulson,A.R., Eperon,I.C., Sanger,F. and Young,I.G. (1982) J. Mol. Biol. 156, 683-717.Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome.Boselaphus tragocamelus (see Aepyceros melampus)Caenorhabditis elegans (see Ascanis suum)Capra hircus (see Antilocapra americana)Cephalophus maxweli (see Aepyceros melampus)Cervus unicolor#Miyamoto,M.M., Kraus,F. and Ryder,O.A. (1990) Proc. Nati. Acad. Sci. U.S.A. 87, 6127-6131.Phylogeny and evolution of antlered deer determined from mitochondrial DNA sequences.Chlamydomonas reinhardtiiBoer,P.H. and Gray,M.W. (1988) Cell 55, 399-411.Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA.#Boer,P.H. and Gray,M.W. (1988) EMBO J. 7, 3501-3508.Genes encoding a subunit of respiratory NADH dehydrogenase (ND1) and a reverse transcriptase-like protein (RTL) are linked to ribosomal RNAgene pieces in Chlamydomonas reinhardtii mitochondrial DNA.#Boer,P.H. and Gray,M.W. (1991) Curr. Genet. 19, 309-312.Short dispersed repeats localized in spacer regions of Chlamydomonas reinhardtii mitochondrial DNA.Crthidia fasciculataSloof,P., Van den Burg,J., Voogd,A., Benne,R., Agostinelli,M., Borst,P., Gutell,R. and Noller,H. (1985) Nucleic Acids Res. 13, 4171-4190.Further characterization of the extremely small mitochondrial ribosomal RNAs from trypanosomes: a detailed comparison of the 9S and 12S RNAsfrom Crithidia fasciculata and Trypanosoma brucei with rRNAs from other organisms.Crithidia oncopelti# Horvath,A., Maslov,D.A. and Kolesnikov,A.A. (1990) Nucleic Acids Res. 18, 281 1.The nucleotide sequence of the 12S ribosomal RNA gene from kinetoplast DNA of the protozoan Crithidia oncopelti.Cyprinus carpio#Chang,Y.S. and Huang,F.I. Unpublished.C. carpio complete mitochondrial genome DNA.Damaliscus dorcas (see Aepyceros melampus)Drosophila melanogaster#Kobayashi,S. and Okada,M. (1990) Nucleic Acids Res. 18, 4592.Complete cDNA sequence encoding mitochondrial large ribosomal RNA of Drosophila melanogaster.Drosophila yakubaClary,D.O. and Wolstenholme,D.R. (1985) Nucleic Acids Res. 13, 4029-4045.The ribosomal RNA genes of Drosophila mitochondrial DNA.Gaflus gallus domesticus#Desjardins,P. and Morais,R. (1990) J. Mol. Biol. 212, 599-634.Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates.Gazella thomsoni (see Aepyceros melampus)Homo sapiensEperon,I.C., Anderson,S. and Nierlich,D.P. (1980) Nature 286, 460-467.Distinctive sequence of human mitochondrial ribosomal RNA genes.Anderson,S., Bankier,A.T., Barrell,B.G., de Bruijn,M.H.L., Coulson,A.R., Drouin,J., Eperon,I.C., Nierlich,D.P., Roe,B.A., Sanger,F., Schreier,P.H.,Smith,A.J.H., Staden,R. and Young,I.G. (1981) Nature 290, 457-465.Sequence and organization of the human mitochondrial genome.Hydropotes inermis (Chinese water deer) (see Cervus unicolor)Kobus eUlipsiprymnus (see Aepyceros melampus)Leishmania tarentolaede la Cruz,V.F., Simpson,A.M., Lake,J.A. and Simpson,L. (1985) Nucleic Acids Res. 13, 2337-2356.Primary sequence and partial secondary structure of the 12S kinetoplast (mitochondrial) ribosomal RNA from Leishmania tarentolae: conservation ofpeptidyl-transferase structural elements.
  12. 12. 2106 Nucleic Acids Research, Vol. 20, SupplementLeptomonas sp.Lake,J.A., de la Cruz,V.F., Ferreira,P.C.G., Morel,C. and Simpson,L. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 4779-4783.Evolution of parasitism: Kinetoplastid protozoan history reconstructed from mitochondrial rRNA gene sequences.Locusta migratoriaUhlenbusch,I., McCracken,A. and Gellissen,G. (1987) Curr. Genet. 11, 631-638.The gene for the large (16S) ribosomal RNA from the Locusta migratoria mitochondrial genome.Madoqua irki (see Aepyceros melampus)Marchania polymorpha#Oda,K., Yamato,K., Ohta,E., Nakamura,Y., Takemura,M., Nozato,N., Akashi,K., Kanegae,T., Ogura,Y., Kohchi,T. and Ohyama,K. (1992) J.Mol. Bio. 223, 1-7.Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA: a primitive form of plant mitochondrialgenome.Muntacus reevesi (see Cervus unicolor)Mus musculusVan Etten,R.A., Walberg,M.W. and Clayton,D.A. (1980) Cell 22, 157-170.Precise localization and nucleotide sequence of the two mouse mitochondrial rRNA genes and three immediately adjacent novel tRNA genes.Bibb,M.J., Van Etten,R.A., Wright,C.T., Walberg,M.W. and Clayton, D.A. (1981) Cell 26, 167-180.Sequence and gene organization of mouse mitochondrial DNA.Neurospora crassa#Abdel-Malik,M.S., Court,D.A., Cheng,C.-K. and Bertrand,H. (1990) Nucleic Acids Res. 18, 7440.Nucleotide sequence of the exons of the large subunit rRNA of Neurospora crassa mitochondria.Odocodeus virginianus (see Cervus unicolor)Oenothera berterianaManna,E. and Brennicke,A. (1985) Curr. Genet. 9, 505-515.Primary and secondary structure of 26S ribosomal RNA of Oenothera mitochondria.Oiyx gazela (see Aepyceros melampus)Paracentrotus liiusCantatore,P., Roberti,M., Rainaldi,G., Gadaleta,M.N. and Saccone,C. (1989) J. Biol. Chem. 264, 10965- 10975.The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.Paramecium pnmaureliaSeilhamer,J.J. and Cummings,D.J. (1981) Nucleic Acids Res. 9, 6391-6406.Structure and sequence of the mitochondrial 20S rRNA and tRNA tyr gene of Paramecium primaurelia.Seilhamer,J.J., Gutell,R.R. and Cummings,D.J. (1984) J. Biol. Chem. 259, 5173-5181.Paramecium mitochondrial genes. II. Large subunit rRNA gene sequence and microevolution.Paramecium tetraurelia (see also Paramecium primaurelia)#Pritchard,A.E., Seilhamer,J.J., Mahalingam,R., Sable,C.L., Venuti,S.E. and Cummings,D.J. (1990) Nucleic Acids Res. 18, 173-180.Nucleotide sequence of the mitochondrial genome of Paramecium.Podospora ansennaCummings,D.J., Domenico,J.M. and Nelson,J. (1989) J. Mol. Evol. 28, 242-255.DNA sequence and secondary structures ofthe large subunit rRNA coding regions and its two class I introns of mitochondrial DNA from Podospora anserina.#Cummings,D.J., McNally,K.L., Domenico,J.M. and Matsuura,E.T. (1990) Curr. Genet. 17, 375-402.The complete DNA sequence of the mitochondrial genome of Podospora anserina.Rana catesbemnaNagae,Y., Fujii,H., Yoneyama,Y., Goto,Y. and Okazaki,T. (1988) Nucleic Acids Res. 16, 10363.Nucleotide sequences of the Rana catesbeiana mitochondrial small (12S) and large (16S) ribosomal RNA genes.Rautus norvegicusSaccone,C., Cantatore,P., Gadaleta,G., Gallerani,R., Lanave,C., Pepe,G. and Kroon,A.M. (1981) Nucleic Acids Res. 9, 4139-4148.The nucleotide sequence of the large ribosomal RNA gene and the adjacent tRNA genes from rat mitochondria.Gadaleta,G., Pepe,G., De Candia, G., Quagliariello,C., Sbisa,E. and Saccone,C. (1989) J. Mol. Evol. 28, 497-516.The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates.Saccharomyces cerevisiaeSor,F. and Fukuhara,H. (1983) Nucleic Acids Res. 11, 339-348.Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria.Schizosaccharomyces pombeLang,B.F., Cedergren,R. and Gray,M.W. (1987) Eur. J. Biochem. 169, 527-537.The mitochondrial genome of the fission yeast, Schizosaccharomycespombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potentialsecondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations.Spodoptera frugiperda#Pashley,D.P. and Ke,L.D. Unpublished.Sequence evolution in the large ribosomal and ND-1 genes in a lepidopteran mitochondrial genome: Implications for phylogenetic analyses.Strongylocentrotus purpuralusJacobs,H.T., Elliott,D.J., Math,V.B. and Farquharson,A. (1988) J. Mol. Biol. 202, 185-217.Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.
  13. 13. Nucleic Acids Research, Vol. 20, Supplement 2107Tetrahymena pynformis#Heinonen,T.Y.K., Schnare,M.N. and Gray,M.W. (1990) J. Biol Chem. 265, 22336-22341.Sequence heterogeneity in the duplicate large subunit ribosomal RNA genes of Tetrahymena pyriformis mitochondrial DNA.Tragelaphus imberbis (see Aepyceros melampus)Tragulus napu (see Antilocapra amencana)Trittcum aesttvumFalconet,D., Sevignac,M. and Quetier,F. (1988) Curr. Genet. 13, 75-82.Nucleotide sequence and determination of the extremities of the 26S ribosomal RNA gene in wheat mitochondria: evidence for sequence rearrangementsin the ribosomal genes of higher plants.Trypanosoma brucei (see Cnthidia fasciculata)Also:Eperon,I.C., Janssen,J.W.G., Hoeijmakers,J.H.J. and Borst,P. (1983) Nucleic Acids Res. 11, 105-125.The major transcripts of the kinetoplast DNA of Trypanosoma brucei are very small ribosomal RNAs.Xenopus laevisRoe,B.A., Ma,D.-P., Wilson,R.K. and Wong,J.F.-H. (1985) J. Biol. Chem. 260, 9759-9774.The complete nucleotide sequence of the Xenopus laevis mitochondrial genome.Zea maysDale,R.M.K., Mendu,N., Ginsburg,H. and Kridl,J.C. (1984) Plasmid 11, 141-150.Sequence analysis of the maize mitochondrial 26 S rRNA gene and flanking regions.EUCARYOTES (NUCLEOCYTOPLASMIC)Arabidopsis thana# Unfried,I. and Gruendler,P. (1990) Nucleic Acids Res. 18, 4011.Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana.Caenorhabditis elegansEllis,R.E., Sulston,J.E. and Coulson,A.R. (1986) Nucleic Acids Res. 14, 2345-2364.The rDNA of C. elegans: sequence and structure.Citrus limonKolosha,V.O. and Fodor,I.I. (1986) Dokl. Akad. Nauk S.S.S.R. 290, 1006-1011.High homology of the nucleotide sequences of the cistron of 26 S rRNA of Citrus limon and Saccharomyces cerevisiae.Kolosha,V.O. and Fodor,I. (1990) Plant Mol. Biol. 14, 147-161.Nucleotide sequence of Citrus linon 26S rRNA gene and secondary structure model of its RNA.Cnithidia fasciculataSpencer,D.F., Collings,J.C., Schnare,M.N. and Gray,M.W. (1987) EMBO J. 6, 1063-1071.Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata.Dictyostelium discoideumOzaki,T., Hoshikawa,Y., Iida,Y. and Iwabuchi,M. (1984) Nucleic Acids Res. 12, 4171-4184.Sequence analysis of the transcribed and 5 non-transcribed regions of the ribosomal RNA gene in Dictyostelium discoideum.Didymium iridisJohansen,S., Johansen,T. and Haugli,F. Unpublished.Extrachromosomal ribosomal DNA of Didymium iridis: sequence analysis of large subunit ribosomal RNA gene and sub-telomeric region.Drosophila melanogasterTautz,D., Hancock,J.M., Webb,D.A., Tautz,C. and Dover,G.A. (1988) Mol. Biol. Evol. 5, 366-376.Complete sequences of the rRNA genes of Drosophila melanogaster.[Minor correction: # Linares,A.R., Hancock,J.M. and Dover,G.A. (1991) J. Mol. Biol. 219, 381-390. Secondary structure constraints on the evolutionof Drosophila 28 S ribosomal RNA expansion segments.]Euglena gracilis#Schnare,M.N. and Gray,M.W. (1990) J. Mol. Biol. 215, 73-83.Sixteen discrete RNA components in the cytoplasmic ribosome of Euglena gracilis.#Schnare,M.N., Cook,J.R. and Gray,M.W. (1990) J. Mol. Biol. 215, 85-91.Fourteen internal transcribed spacers in the circular ribosomal DNA of Euglena gracilis.Fragaria ananassa# Simovic,N., Wolyn,D. and Jelenkovic,G. Unpublished.Strawberry (octoploid) DNA for 5.8S ribosomal RNA.# Simovic,N. and Jelenkovic,G. Unpublished.The nucleotide sequence of 26S rDNA gene isolated from Fragariaxananassa Duch.-cultivated octoploid strawberry.Giardia ardeae#van Keulen,H., Horvat,S., Erlandsen,S.L. and Jarroll,E.L. (1991) Nucleic Acids Res. 19, 6050.Nucleotide sequence of the 5.8S and large subunit rRNA genes and the internal transcribed spacer and part of the external spacer from Giardia ardeae.Giardia intestinals#Healey,A., Mitchell,R., Upcroft,J.A., Boreham,P.F.L. and Upcroft,P. (1990) Nucleic Acids Res. 18, 4006.Complete nucleotide sequence of the ribosomal RNA tandem repeat unit from Giardia intestinalis.Herdmania momus#Degnan,B.M., Yan,J., Hawkins,C.J. and Lavin,M.F. (1990) Nucleic Acids Res. 18, 7063-7070.rRNA genes from the lower chordate Herdmania momus: structural similarity with higher eukaryotes.
  14. 14. 2108 Nucleic Acids Research, Vol. 20, SupplementHomo sapiens#Maden,B.E.H., Dent,C.L., Farrell,T.E., Garde,J., McCallum,F.S. and Wakeman,J.A. (1987) Biochem J. 246, 519-527.Clones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the human ribosomaltranscription unit and diversity among clones.[Correction to eliminate extra GC (following posiiion 50) in the original 5.8S rRNA sequence of Khan,M.S. N and Maden,B.E.H. (1977) Nucleic AcidsRes. 4, 2495-2505. Nucleotide sequence relationships between vertebrate 5.8 S ribosomal RNAs.]Gonzalez,I.L., Gorski,J.L., Campen,T.J., Dorney,D.J., Erickson,J.M., Sylvester,J.E. and Schmickel,R.D. (1985) Proc. Natl. Acad. Sci. U.S.A. 82,7666-7670.Variation among human 28S ribosomal RNA genes.Lycopersicon esculentumKiss,T., Kis,M., Abel,S. and Solymosy,F. (1988) Nucleic Acids Res. 16, 7179.Nucleotide sequence of the 17S-25S spacer region from tomato rDNA.Kiss,T., Kis,M. and Solymosy,F. (1989) Nucleic Acids Res. 17, 796.Nucleotide sequence of a 25S rRNA gene from tomato.Mucor racemosus#Ji,G.E. and Orlowski,M. (1990) Curr. Genet. 17, 499-506.Primary and secondary structure of the 25S rRNA from the dimorphic fungus Mucor racemosus.Mus musculusMichot,B., Bachellerie,J.-P. and Raynal,F. (1982) Nucleic Acids Res. 10, 5273-5283.Sequence and secondary structure of mouse 28S rRNA 5terminal domain. Organisation of the 5.8S-28S rRNA complex.Hassouna,N., Michot,B. and Bachellerie,J.-P. (1984) Nucleic Acids Res. 12, 3563-3583.The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes.Oryza saivaTakaiwa,F., Oono,K. and Sugiura,M. (1985) Plant Mol. Biol. 4, 355-364.Nucleotide sequence of the 17S-25S spacer region from rice rDNA.Takaiwa,F., Oono,K., lida,Y. and Sugiura,M. (1985) Gene 37, 255-259.The complete nucleotide sequence of a rice 25S rRNA gene.Physarum polycephalumOtsuka,T., Nomiyama,H., Yoshida,H., Kukita,T., Kuhara,S. and Sakaki,Y. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 3163-3167.Complete nucleotide sequence of the 26S rRNA gene of Physarum polycephalum: Its significance in gene evolution.Prorocentrum micansMaroteaux,L., Herzog,M. and Soyer-Gobillard,M.-O. (1985) BioSystems 18, 307-319.Molecular organization of dinoflagellate ribosomal DNA: evolutionary implications of the deduced 5.8S rRNA secondary structure.Lenaers,G., Maroteaux,L., Michot,B. and Herzog,M. (1989) J. Mol. Evol. 29, 40-51.Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA.Rattus norvegicusSubrahmanyam,C.S., Cassidy,B., Busch,H. and Rothblum,L.I. (1982) Nucleic Acids Res. 10, 3667-3680.Nucleotide sequence of the region between the 18S rRNA sequence and the 28S rRNA sequence of rat ribosomal DNA.Chan,Y.-L., Olvera,J. and Wool,I.G. (1983) Nucleic Acids Res. 11, 7819-7831.The structure of rat 28S ribosomal ribonucleic acid inferred from the sequence of nucleotides in a gene.Hadjiolov,A.A., Georgiev,O.I., Nosikov,V.V. and Yavachev,L.P. (1984) Nucleic Acids Res. 12, 3677-3693.Primary and secondary structure of rat 28 S ribosomal RNA.Wool,I.G. (1986) In Hardesty,B. and Kramer,G. (eds.). Structure, Function, and Genetics ofRibosomes. Springer-Verlag, New York, pp. 391 -411.Studies on the structure of eukaryotic (mammalian) ribosomes.Saccharomyces carisbergensisVeldman,G.M., Klootwijk,J., de Regt,V.C.H.F., Planta,R.J., Branlant,C., Krol,A. and Ebel,J.-P. (1981) Nucleic Acids Res. 9, 6935-6952.The primary and secondary structure of yeast 26S rRNA.Saccharomyces cerevisiaeRubin,G.M. (1973) J. Biol. Chem. 248, 3860-3875.The nucleotide sequence of Saccharomyces cerevisiae 5.8 S ribosomal ribonucleic acid.Georgiev,O.., Nikolaev,N., Hadjiolov,A.A., Skryabin,K.G., Zakharyev,V.M. and Bayev,A.A. (1981) Nucleic Acids Res. 9, 6953-6958.The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisiae.Sinapsis alba# Capesius,I. (1991) Plant Mol. Biol. 16, 1093-1094.Nucleotide sequence of a 25S rRNA gene from mustard (Sinapsis alba).# Rathgeber,J. and Capesius,I. (1989) Nucleic Acids Res. 17, 7522.Nucleotide sequence of the 18S-25S spacer region from mustard DNA.Tetrahymena pyriformis#Engberg,J., Nielsen,H., Lenaers,G., Murayama,O., Fujitani,H. and Higashinakagawa,T. (1990) J. Mol. Evol. 30, 514-521.Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: Evidence for a strong evolutionary and structural contraintin expansion segments.Tetrahymena thermophila (see also Tetrahymena pyriformis)#Engberg,J. and Nielsen,H. (1990) Nucleic Acids Res. 18, 6915-6919.Complete sequence of the extrachromosomal rDNA molecule from the ciliate Tetrahymena thermophila strain B1868VI1.
  15. 15. Nucleic Acids Research, Vol. 20, Supplement 2109Trypanosoma brucei# Campbell,D. Unpublished.Trypanosoma brucei gene for ribosomal RNA large subunit.#Campbell,D.A., Kubo, K., Clark,C.G. and Boothroyd,J.C. (1987) J. Mol. Biol. 196, 113-124.Precise identification of cleavage sites involved in the unusual processing of trypanosome ribosomal RNA.#White,T.C., Rudenko,G. and Borst,P. (1986) Nucleic Acids Res. 14, 9471-9489.Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to Domain VII of other eukaryotic 28S rRNAs.Xenopus borealis#Ajuh,P.M., Heeney,P.A. and Maden,B.E.H. (1991) Proc. R. Soc. Lond., B, Biol. Sci. 245, 65-71.Xenopus borealis and Xenopus laevis 28S ribosomal DNA and the complete 40S ribosomal precursor RNA coding units of both species.Xenopus laevis (see also Xenopus borealis)Hall,L.M.C. and Maden,B.E.H. (1980) Nucleic Acids Res. 8, 5993-6005.Nucleotide sequence through the 18S-28S intergene region of a vertebrate ribosomal transcription unit.Ware,V.C., Tague,B.W., Clark,C.G., Gourse,R.L., Brand,R.C.and Gerbi,S.A. (1983) Nucleic Acids Res. 11, 7795-7817.Sequence analysis of 28S ribosomal DNA from the amphibian Xenopus laevis.[Corrections to sequence of Domain V: # Stebbins-Boaz,B. and Gerbi,S.A. (1991) J. Mol. Biol. 217, 93- 112. Structural analysis of the peptidyl transferaseregion in ribosomal RNA of the eukaryote Xenopus laevis.]# Schnare,M.N. and Gray,M.W. (1992) Nucleic Acids Res. 20, in press.A new 3-terminus for Xenopus laevis 28S ribosomal RNA.