The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications
Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of diverge...
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| Veröffentlicht in: | Genetics (Austin) 1997-03, Vol.145 (3), p.821-832 |
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| creator | Buckler, E.S. IV Ippolito, A Holtsford, T.P |
| description | Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies. |
| doi_str_mv | 10.1093/genetics/145.3.821 |
| format | Article |
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IV ; Ippolito, A ; Holtsford, T.P</creator><creatorcontrib>Buckler, E.S. IV ; Ippolito, A ; Holtsford, T.P</creatorcontrib><description>Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.</description><identifier>ISSN: 0016-6731</identifier><identifier>ISSN: 1943-2631</identifier><identifier>EISSN: 1943-2631</identifier><identifier>DOI: 10.1093/genetics/145.3.821</identifier><identifier>PMID: 9055091</identifier><identifier>CODEN: GENTAE</identifier><language>eng</language><publisher>United States: Genetics Soc America</publisher><subject>ADN ; ALLELES ; Deoxyribonucleic acid ; DNA ; DNA CONFORMATION ; DNA, Ribosomal - genetics ; Evolution ; Evolution, Molecular ; Flowers & plants ; GENE ; GENES ; Genetics ; GOSSYPIUM ; Gossypium hirsutum ; GRAMINEAE ; INTERNAL TRANSCRIBED SPACER ; Investigations ; NICOTIANA ; Nicotiana tabacum ; NUCLEOTIDE SEQUENCE ; PCR ; Phylogeny ; Plants - genetics ; POACEAE ; POLYMERASE CHAIN REACTION ; PSEUDOGENE ; PSEUDOGENES ; RANALES ; RECOMBINACION ; RECOMBINAISON ; RECOMBINATION ; Recombination, Genetic ; RIBOSOMAS ; RIBOSOME ; RIBOSOMES ; SECONDARY STRUCTURE ; SECUENCIA NUCLEOTIDICA ; SEQUENCE NUCLEOTIDIQUE ; SEUDOGENES ; Tripsacum dactyloides ; WINTERACEAE ; ZEA ; Zea mays</subject><ispartof>Genetics (Austin), 1997-03, Vol.145 (3), p.821-832</ispartof><rights>Copyright Genetics Society of America Mar 1997</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c574t-e4a43fe0911e77bd6c2f03e085735fa28d30603340e4ae576ebc870d985cf8e33</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9055091$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Buckler, E.S. IV</creatorcontrib><creatorcontrib>Ippolito, A</creatorcontrib><creatorcontrib>Holtsford, T.P</creatorcontrib><title>The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications</title><title>Genetics (Austin)</title><addtitle>Genetics</addtitle><description>Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.</description><subject>ADN</subject><subject>ALLELES</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA CONFORMATION</subject><subject>DNA, Ribosomal - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Flowers & plants</subject><subject>GENE</subject><subject>GENES</subject><subject>Genetics</subject><subject>GOSSYPIUM</subject><subject>Gossypium hirsutum</subject><subject>GRAMINEAE</subject><subject>INTERNAL TRANSCRIBED SPACER</subject><subject>Investigations</subject><subject>NICOTIANA</subject><subject>Nicotiana tabacum</subject><subject>NUCLEOTIDE SEQUENCE</subject><subject>PCR</subject><subject>Phylogeny</subject><subject>Plants - genetics</subject><subject>POACEAE</subject><subject>POLYMERASE CHAIN REACTION</subject><subject>PSEUDOGENE</subject><subject>PSEUDOGENES</subject><subject>RANALES</subject><subject>RECOMBINACION</subject><subject>RECOMBINAISON</subject><subject>RECOMBINATION</subject><subject>Recombination, Genetic</subject><subject>RIBOSOMAS</subject><subject>RIBOSOME</subject><subject>RIBOSOMES</subject><subject>SECONDARY STRUCTURE</subject><subject>SECUENCIA NUCLEOTIDICA</subject><subject>SEQUENCE NUCLEOTIDIQUE</subject><subject>SEUDOGENES</subject><subject>Tripsacum dactyloides</subject><subject>WINTERACEAE</subject><subject>ZEA</subject><subject>Zea mays</subject><issn>0016-6731</issn><issn>1943-2631</issn><issn>1943-2631</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1997</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkluL1DAYhoMo67j6BwSheLF3nf2-pM3BC2FZj7Ao6O51yLRpm6VtatLOsP_ejDOuBwSvQsiTN0_yhpDnCGsExc5bO9rZVfEci3LN1pLiA7JCVbCccoYPyQoAec4Fw8fkSYy3AMBVKU_IiYKyBIUr8uW6s5nd-n6ZnR8z32TBbXz0g-mzN58uXmW129qQDpqzyQTT-3axMTNjnU3dXZodDDI3TL2rzD4jPiWPGtNH--w4npKbd2-vLz_kV5_ff7y8uMqrUhRzbgtTsMYmC7RCbGpe0QaYBVkKVjaGypoBB8YKSKQtBbebSgqolSyrRlrGTsnrQ-60bAZbV8kxCeopuMGEO-2N03-ujK7Trd9qpCAk5yng7BgQ_Ld0rVkPLla2781o_RK1kFJwQPVfEJMnFRIT-PIv8NYvYUyvoCkWSEVB9xA9QFXwMQbb3Csj6H2v-mevOvWqmZY_Nr34_bL3W45F_lLsXNvtXLA6pgr7RKPe7Xb_CGqM16YNLuqbr6iUAJE-jWTfAXgkt7A</recordid><startdate>199703</startdate><enddate>199703</enddate><creator>Buckler, E.S. IV</creator><creator>Ippolito, A</creator><creator>Holtsford, T.P</creator><general>Genetics Soc America</general><general>Genetics Society of America</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>4T-</scope><scope>4U-</scope><scope>7QP</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>199703</creationdate><title>The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications</title><author>Buckler, E.S. IV ; Ippolito, A ; Holtsford, T.P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c574t-e4a43fe0911e77bd6c2f03e085735fa28d30603340e4ae576ebc870d985cf8e33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1997</creationdate><topic>ADN</topic><topic>ALLELES</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA CONFORMATION</topic><topic>DNA, Ribosomal - genetics</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Flowers & plants</topic><topic>GENE</topic><topic>GENES</topic><topic>Genetics</topic><topic>GOSSYPIUM</topic><topic>Gossypium hirsutum</topic><topic>GRAMINEAE</topic><topic>INTERNAL TRANSCRIBED SPACER</topic><topic>Investigations</topic><topic>NICOTIANA</topic><topic>Nicotiana tabacum</topic><topic>NUCLEOTIDE SEQUENCE</topic><topic>PCR</topic><topic>Phylogeny</topic><topic>Plants - genetics</topic><topic>POACEAE</topic><topic>POLYMERASE CHAIN REACTION</topic><topic>PSEUDOGENE</topic><topic>PSEUDOGENES</topic><topic>RANALES</topic><topic>RECOMBINACION</topic><topic>RECOMBINAISON</topic><topic>RECOMBINATION</topic><topic>Recombination, Genetic</topic><topic>RIBOSOMAS</topic><topic>RIBOSOME</topic><topic>RIBOSOMES</topic><topic>SECONDARY STRUCTURE</topic><topic>SECUENCIA NUCLEOTIDICA</topic><topic>SEQUENCE NUCLEOTIDIQUE</topic><topic>SEUDOGENES</topic><topic>Tripsacum dactyloides</topic><topic>WINTERACEAE</topic><topic>ZEA</topic><topic>Zea mays</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Buckler, E.S. IV</creatorcontrib><creatorcontrib>Ippolito, A</creatorcontrib><creatorcontrib>Holtsford, T.P</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Docstoc</collection><collection>University Readers</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genetics (Austin)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Buckler, E.S. IV</au><au>Ippolito, A</au><au>Holtsford, T.P</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications</atitle><jtitle>Genetics (Austin)</jtitle><addtitle>Genetics</addtitle><date>1997-03</date><risdate>1997</risdate><volume>145</volume><issue>3</issue><spage>821</spage><epage>832</epage><pages>821-832</pages><issn>0016-6731</issn><issn>1943-2631</issn><eissn>1943-2631</eissn><coden>GENTAE</coden><abstract>Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.</abstract><cop>United States</cop><pub>Genetics Soc America</pub><pmid>9055091</pmid><doi>10.1093/genetics/145.3.821</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0016-6731 |
| ispartof | Genetics (Austin), 1997-03, Vol.145 (3), p.821-832 |
| issn | 0016-6731 1943-2631 1943-2631 |
| language | eng |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford University Press Journals All Titles (1996-Current); Alma/SFX Local Collection |
| subjects | ADN ALLELES Deoxyribonucleic acid DNA DNA CONFORMATION DNA, Ribosomal - genetics Evolution Evolution, Molecular Flowers & plants GENE GENES Genetics GOSSYPIUM Gossypium hirsutum GRAMINEAE INTERNAL TRANSCRIBED SPACER Investigations NICOTIANA Nicotiana tabacum NUCLEOTIDE SEQUENCE PCR Phylogeny Plants - genetics POACEAE POLYMERASE CHAIN REACTION PSEUDOGENE PSEUDOGENES RANALES RECOMBINACION RECOMBINAISON RECOMBINATION Recombination, Genetic RIBOSOMAS RIBOSOME RIBOSOMES SECONDARY STRUCTURE SECUENCIA NUCLEOTIDICA SEQUENCE NUCLEOTIDIQUE SEUDOGENES Tripsacum dactyloides WINTERACEAE ZEA Zea mays |
| title | The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications |
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