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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 |
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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 |
format | article |
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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&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. A. Cara</creatorcontrib><creatorcontrib>Okura, Vagner K.</creatorcontrib><creatorcontrib>Felipe R. da Silva</creatorcontrib><creatorcontrib>Guilherme L. Pedrosa</creatorcontrib><creatorcontrib>Hemerly, Adriana S.</creatorcontrib><creatorcontrib>Adriana N. Capella</creatorcontrib><creatorcontrib>Marins, Mozart</creatorcontrib><creatorcontrib>Ferreira, Paulo C.</creatorcontrib><creatorcontrib>Suzelei C. França</creatorcontrib><creatorcontrib>Laurent Grivet</creatorcontrib><creatorcontrib>Vettore, Andre L.</creatorcontrib><creatorcontrib>Kemper, Edson L.</creatorcontrib><creatorcontrib>Willian L. Burnquist</creatorcontrib><creatorcontrib>Maria L. P. Targon</creatorcontrib><creatorcontrib>Walter J. Siqueira</creatorcontrib><creatorcontrib>Eiko E. Kuramae</creatorcontrib><creatorcontrib>Celso L. Marino</creatorcontrib><creatorcontrib>Luis E. A. Camargo</creatorcontrib><creatorcontrib>Carrer, Helaine</creatorcontrib><creatorcontrib>Luis L. Coutinho</creatorcontrib><creatorcontrib>Luiz R. Furlan</creatorcontrib><creatorcontrib>Manoel V. F. Lemos</creatorcontrib><creatorcontrib>Luiz R. Nunes</creatorcontrib><creatorcontrib>Suely L. Gomes</creatorcontrib><creatorcontrib>Santelli, Roberto V.</creatorcontrib><creatorcontrib>Maria H. Goldman</creatorcontrib><creatorcontrib>Maurício Bacci Jr</creatorcontrib><creatorcontrib>Eder A. Giglioti</creatorcontrib><creatorcontrib>Thiemann, Otávio H.</creatorcontrib><creatorcontrib>Flávio H. Silva</creatorcontrib><creatorcontrib>Marie-Anne Van Sluys</creatorcontrib><creatorcontrib>Nobrega, Francisco G.</creatorcontrib><creatorcontrib>Arruda, Paulo</creatorcontrib><creatorcontrib>Carlos F. M. 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. Technologies</subject><subject>Oryza - classification</subject><subject>Oryza - genetics</subject><subject>Oryza sativa</subject><subject>Plant breeding: fundamental aspects and methodology</subject><subject>Plants</subject><subject>Plants genetics</subject><subject>Qualitative comparative analysis</subject><subject>Rice</subject><subject>Saccharum - classification</subject><subject>Saccharum - genetics</subject><subject>Saccharum officinarum</subject><subject>Sugar cane</subject><subject>Transcription, Genetic</subject><subject>Transcriptomes</subject><subject>Transgenic animals and transgenic plants</subject><subject>Transgenic plants</subject><issn>0032-0889</issn><issn>1532-2548</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><recordid>eNqF0ctP3DAQB2CrApXlceRWVbm0EocsHr9zRHR5SEt7AM6W43UWo2wc7GSl_vf1KivojZN_sj-Pxh6EzgHPATC77Ps5YDrHlCqpvqAZcEpKwpk6QDOMc8ZKVUfoOKVXjDFQYF_REXBMsOTVDP1ebE07msGHrghN8RC6YMNQmG5VLMaV3-Vffuvi2nXWFc_Jd-tieHHF47g20ZrOFU_RdMlG3w9h407RYWPa5M726wl6vlk8Xd-Vyz-399dXy9IyRYZSCFMTphgzwvCmrimjCtcCnIWGUbFiogJpGimFwJZytntUvkGBgFCOcXqCLqa6L6bVffQbE__qYLy-u1rq3R4mQlECfAvZ_pxsH8Pb6NKgNz5Z17a5-zAmLUESRbn6FIKsCJGMZlhO0MaQUnTNewuA9W4quu9zpHqaSvbf94XHeuNWH3o_hgx-7IFJ1rRN_lLr03-OV4RLmd23yb2mIcT3c0YUCFLRf1X1m20</recordid><startdate>20040301</startdate><enddate>20040301</enddate><creator>Vincentz, Michel</creator><creator>Frank A. A. Cara</creator><creator>Okura, Vagner K.</creator><creator>Felipe R. da Silva</creator><creator>Guilherme L. Pedrosa</creator><creator>Hemerly, Adriana S.</creator><creator>Adriana N. Capella</creator><creator>Marins, Mozart</creator><creator>Ferreira, Paulo C.</creator><creator>Suzelei C. França</creator><creator>Laurent Grivet</creator><creator>Vettore, Andre L.</creator><creator>Kemper, Edson L.</creator><creator>Willian L. Burnquist</creator><creator>Maria L. P. Targon</creator><creator>Walter J. Siqueira</creator><creator>Eiko E. Kuramae</creator><creator>Celso L. Marino</creator><creator>Luis E. A. Camargo</creator><creator>Carrer, Helaine</creator><creator>Luis L. Coutinho</creator><creator>Luiz R. Furlan</creator><creator>Manoel V. F. Lemos</creator><creator>Luiz R. Nunes</creator><creator>Suely L. Gomes</creator><creator>Santelli, Roberto V.</creator><creator>Maria H. Goldman</creator><creator>Maurício Bacci Jr</creator><creator>Eder A. Giglioti</creator><creator>Thiemann, Otávio H.</creator><creator>Flávio H. Silva</creator><creator>Marie-Anne Van Sluys</creator><creator>Nobrega, Francisco G.</creator><creator>Arruda, Paulo</creator><creator>Carlos F. M. Menck</creator><general>American Society of Plant Biologists</general><general>American Society of Plant Physiologists</general><general>Oxford University Press ; American Society of Plant Biologists</general><scope>IQODW</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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>1XC</scope></search><sort><creationdate>20040301</creationdate><title>Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome</title><author>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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c482t-66ab24844a6a5fbb34380b61ec1f436d46917af77660c3541532ab2312168e453</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Agronomy. Soil science and plant productions</topic><topic>Angiosperms</topic><topic>Arabidopsis</topic><topic>Arabidopsis - classification</topic><topic>Arabidopsis - genetics</topic><topic>Biological and medical sciences</topic><topic>Biotechnology</topic><topic>Chromosomes, Plant - genetics</topic><topic>Consensus Sequence</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Evolutionary genetics</topic><topic>Expressed Sequence Tags</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes</topic><topic>Genetic engineering</topic><topic>Genetic engineering applications</topic><topic>Genetic technics</topic><topic>Genetics</topic><topic>Genetics and breeding of economic plants</topic><topic>Genome Analysis</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>Life Sciences</topic><topic>Magnoliopsida - classification</topic><topic>Magnoliopsida - genetics</topic><topic>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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recordid | cdi_hal_primary_oai_HAL_hal_02683215v1 |
source | JSTOR Archival Journals and Primary Sources Collection; Oxford Journals - Connect here FIRST to enable access |
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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