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Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcript...

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Published in:Plant physiology (Bethesda) 2004-03, Vol.134 (3), p.951-959
Main Authors: Vincentz, Michel, Frank A. A. Cara, Okura, Vagner K., Felipe R. da Silva, Guilherme L. Pedrosa, Hemerly, Adriana S., Adriana N. Capella, Marins, Mozart, Ferreira, Paulo C., Suzelei C. França, Laurent Grivet, Vettore, Andre L., Kemper, Edson L., Willian L. Burnquist, Maria L. P. Targon, Walter J. Siqueira, Eiko E. Kuramae, Celso L. Marino, Luis E. A. Camargo, Carrer, Helaine, Luis L. Coutinho, Luiz R. Furlan, Manoel V. F. Lemos, Luiz R. Nunes, Suely L. Gomes, Santelli, Roberto V., Maria H. Goldman, Maurício Bacci Jr, Eder A. Giglioti, Thiemann, Otávio H., Flávio H. Silva, Marie-Anne Van Sluys, Nobrega, Francisco G., Arruda, Paulo, Carlos F. M. Menck
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cited_by cdi_FETCH-LOGICAL-c482t-66ab24844a6a5fbb34380b61ec1f436d46917af77660c3541532ab2312168e453
cites cdi_FETCH-LOGICAL-c482t-66ab24844a6a5fbb34380b61ec1f436d46917af77660c3541532ab2312168e453
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container_title Plant physiology (Bethesda)
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creator Vincentz, Michel
Frank A. A. Cara
Okura, Vagner K.
Felipe R. da Silva
Guilherme L. Pedrosa
Hemerly, Adriana S.
Adriana N. Capella
Marins, Mozart
Ferreira, Paulo C.
Suzelei C. França
Laurent Grivet
Vettore, Andre L.
Kemper, Edson L.
Willian L. Burnquist
Maria L. P. Targon
Walter J. Siqueira
Eiko E. Kuramae
Celso L. Marino
Luis E. A. Camargo
Carrer, Helaine
Luis L. Coutinho
Luiz R. Furlan
Manoel V. F. Lemos
Luiz R. Nunes
Suely L. Gomes
Santelli, Roberto V.
Maria H. Goldman
Maurício Bacci Jr
Eder A. Giglioti
Thiemann, Otávio H.
Flávio H. Silva
Marie-Anne Van Sluys
Nobrega, Francisco G.
Arruda, Paulo
Carlos F. M. Menck
description Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.
doi_str_mv 10.1104/pp.103.033878
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A. Cara ; Okura, Vagner K. ; Felipe R. da Silva ; Guilherme L. Pedrosa ; Hemerly, Adriana S. ; Adriana N. Capella ; Marins, Mozart ; Ferreira, Paulo C. ; Suzelei C. França ; Laurent Grivet ; Vettore, Andre L. ; Kemper, Edson L. ; Willian L. Burnquist ; Maria L. P. Targon ; Walter J. Siqueira ; Eiko E. Kuramae ; Celso L. Marino ; Luis E. A. Camargo ; Carrer, Helaine ; Luis L. Coutinho ; Luiz R. Furlan ; Manoel V. F. Lemos ; Luiz R. Nunes ; Suely L. Gomes ; Santelli, Roberto V. ; Maria H. Goldman ; Maurício Bacci Jr ; Eder A. Giglioti ; Thiemann, Otávio H. ; Flávio H. Silva ; Marie-Anne Van Sluys ; Nobrega, Francisco G. ; Arruda, Paulo ; Carlos F. M. Menck</creator><creatorcontrib>Vincentz, Michel ; Frank A. A. Cara ; Okura, Vagner K. ; Felipe R. da Silva ; Guilherme L. Pedrosa ; Hemerly, Adriana S. ; Adriana N. Capella ; Marins, Mozart ; Ferreira, Paulo C. ; Suzelei C. França ; Laurent Grivet ; Vettore, Andre L. ; Kemper, Edson L. ; Willian L. Burnquist ; Maria L. P. Targon ; Walter J. Siqueira ; Eiko E. Kuramae ; Celso L. Marino ; Luis E. A. Camargo ; Carrer, Helaine ; Luis L. Coutinho ; Luiz R. Furlan ; Manoel V. F. Lemos ; Luiz R. Nunes ; Suely L. Gomes ; Santelli, Roberto V. ; Maria H. Goldman ; Maurício Bacci Jr ; Eder A. Giglioti ; Thiemann, Otávio H. ; Flávio H. Silva ; Marie-Anne Van Sluys ; Nobrega, Francisco G. ; Arruda, Paulo ; Carlos F. M. Menck</creatorcontrib><description>Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.</description><identifier>ISSN: 0032-0889</identifier><identifier>EISSN: 1532-2548</identifier><identifier>DOI: 10.1104/pp.103.033878</identifier><identifier>PMID: 15020759</identifier><identifier>CODEN: PPHYA5</identifier><language>eng</language><publisher>Rockville, MD: American Society of Plant Biologists</publisher><subject>Agronomy. Soil science and plant productions ; Angiosperms ; Arabidopsis ; Arabidopsis - classification ; Arabidopsis - genetics ; Biological and medical sciences ; Biotechnology ; Chromosomes, Plant - genetics ; Consensus Sequence ; Evolution ; Evolution, Molecular ; Evolutionary genetics ; Expressed Sequence Tags ; Fundamental and applied biological sciences. Psychology ; Genes ; Genetic engineering ; Genetic engineering applications ; Genetic technics ; Genetics ; Genetics and breeding of economic plants ; Genome Analysis ; Genome, Plant ; Genomes ; Life Sciences ; Magnoliopsida - classification ; Magnoliopsida - genetics ; Methods. Procedures. Technologies ; Oryza - classification ; Oryza - genetics ; Oryza sativa ; Plant breeding: fundamental aspects and methodology ; Plants ; Plants genetics ; Qualitative comparative analysis ; Rice ; Saccharum - classification ; Saccharum - genetics ; Saccharum officinarum ; Sugar cane ; Transcription, Genetic ; Transcriptomes ; Transgenic animals and transgenic plants ; Transgenic plants</subject><ispartof>Plant physiology (Bethesda), 2004-03, Vol.134 (3), p.951-959</ispartof><rights>Copyright 2004 American Society of Plant Biologists</rights><rights>2004 INIST-CNRS</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c482t-66ab24844a6a5fbb34380b61ec1f436d46917af77660c3541532ab2312168e453</citedby><cites>FETCH-LOGICAL-c482t-66ab24844a6a5fbb34380b61ec1f436d46917af77660c3541532ab2312168e453</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/4281629$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/4281629$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,315,786,790,891,27957,27958,58593,58826</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&amp;idt=15592577$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15020759$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.inrae.fr/hal-02683215$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Vincentz, Michel</creatorcontrib><creatorcontrib>Frank A. 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Menck</creatorcontrib><title>Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome</title><title>Plant physiology (Bethesda)</title><addtitle>Plant Physiol</addtitle><description>Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.</description><subject>Agronomy. Soil science and plant productions</subject><subject>Angiosperms</subject><subject>Arabidopsis</subject><subject>Arabidopsis - classification</subject><subject>Arabidopsis - genetics</subject><subject>Biological and medical sciences</subject><subject>Biotechnology</subject><subject>Chromosomes, Plant - genetics</subject><subject>Consensus Sequence</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Evolutionary genetics</subject><subject>Expressed Sequence Tags</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes</subject><subject>Genetic engineering</subject><subject>Genetic engineering applications</subject><subject>Genetic technics</subject><subject>Genetics</subject><subject>Genetics and breeding of economic plants</subject><subject>Genome Analysis</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Life Sciences</subject><subject>Magnoliopsida - classification</subject><subject>Magnoliopsida - genetics</subject><subject>Methods. Procedures. 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Menck</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome</atitle><jtitle>Plant physiology (Bethesda)</jtitle><addtitle>Plant Physiol</addtitle><date>2004-03-01</date><risdate>2004</risdate><volume>134</volume><issue>3</issue><spage>951</spage><epage>959</epage><pages>951-959</pages><issn>0032-0889</issn><eissn>1532-2548</eissn><coden>PPHYA5</coden><notes>ObjectType-Article-2</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-1</notes><notes>content type line 23</notes><notes>ObjectType-Article-1</notes><notes>ObjectType-Feature-2</notes><notes>PMCID: PMC389918</notes><abstract>Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.</abstract><cop>Rockville, MD</cop><pub>American Society of Plant Biologists</pub><pmid>15020759</pmid><doi>10.1104/pp.103.033878</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record>
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subjects Agronomy. Soil science and plant productions
Angiosperms
Arabidopsis
Arabidopsis - classification
Arabidopsis - genetics
Biological and medical sciences
Biotechnology
Chromosomes, Plant - genetics
Consensus Sequence
Evolution
Evolution, Molecular
Evolutionary genetics
Expressed Sequence Tags
Fundamental and applied biological sciences. Psychology
Genes
Genetic engineering
Genetic engineering applications
Genetic technics
Genetics
Genetics and breeding of economic plants
Genome Analysis
Genome, Plant
Genomes
Life Sciences
Magnoliopsida - classification
Magnoliopsida - genetics
Methods. Procedures. Technologies
Oryza - classification
Oryza - genetics
Oryza sativa
Plant breeding: fundamental aspects and methodology
Plants
Plants genetics
Qualitative comparative analysis
Rice
Saccharum - classification
Saccharum - genetics
Saccharum officinarum
Sugar cane
Transcription, Genetic
Transcriptomes
Transgenic animals and transgenic plants
Transgenic plants
title Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome
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