Why Assembling Plant Genome Sequences Is So Challenging
Identifieur interne : 000451 ( Main/Exploration ); précédent : 000450; suivant : 000452Why Assembling Plant Genome Sequences Is So Challenging
Auteurs : Manuel Gonzalo Claros ; Rocío Bautista ; Darío Guerrero-Fernández ; Hicham Benzerki ; Pedro Seoane ; Noé Fernández-PozoSource :
- Biology [ 2079-7737 ] ; 2012.
Abstract
In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.
Url:
DOI: 10.3390/biology1020439
PubMed: 24832233
PubMed Central: 4009782
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Why Assembling Plant Genome Sequences Is So Challenging</title><author><name sortKey="Claros, Manuel Gonzalo" sort="Claros, Manuel Gonzalo" uniqKey="Claros M" first="Manuel Gonzalo" last="Claros">Manuel Gonzalo Claros</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Bautista, Rocio" sort="Bautista, Rocio" uniqKey="Bautista R" first="Rocío" last="Bautista">Rocío Bautista</name><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Guerrero Fernandez, Dario" sort="Guerrero Fernandez, Dario" uniqKey="Guerrero Fernandez D" first="Darío" last="Guerrero-Fernández">Darío Guerrero-Fernández</name><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Benzerki, Hicham" sort="Benzerki, Hicham" uniqKey="Benzerki H" first="Hicham" last="Benzerki">Hicham Benzerki</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Seoane, Pedro" sort="Seoane, Pedro" uniqKey="Seoane P" first="Pedro" last="Seoane">Pedro Seoane</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation></author><author><name sortKey="Fernandez Pozo, Noe" sort="Fernandez Pozo, Noe" uniqKey="Fernandez Pozo N" first="Noé" last="Fernández-Pozo">Noé Fernández-Pozo</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24832233</idno><idno type="pmc">4009782</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009782</idno><idno type="RBID">PMC:4009782</idno><idno type="doi">10.3390/biology1020439</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000697</idno><idno type="wicri:Area/Pmc/Curation">000697</idno><idno type="wicri:Area/Pmc/Checkpoint">000362</idno><idno type="wicri:Area/Ncbi/Merge">000520</idno><idno type="wicri:Area/Ncbi/Curation">000520</idno><idno type="wicri:Area/Ncbi/Checkpoint">000520</idno><idno type="wicri:Area/Main/Merge">000452</idno><idno type="wicri:Area/Main/Curation">000451</idno><idno type="wicri:Area/Main/Exploration">000451</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Why Assembling Plant Genome Sequences Is So Challenging</title><author><name sortKey="Claros, Manuel Gonzalo" sort="Claros, Manuel Gonzalo" uniqKey="Claros M" first="Manuel Gonzalo" last="Claros">Manuel Gonzalo Claros</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Bautista, Rocio" sort="Bautista, Rocio" uniqKey="Bautista R" first="Rocío" last="Bautista">Rocío Bautista</name><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Guerrero Fernandez, Dario" sort="Guerrero Fernandez, Dario" uniqKey="Guerrero Fernandez D" first="Darío" last="Guerrero-Fernández">Darío Guerrero-Fernández</name><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Benzerki, Hicham" sort="Benzerki, Hicham" uniqKey="Benzerki H" first="Hicham" last="Benzerki">Hicham Benzerki</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-biology-01-00439">Bioinformatics Andalusian Platform, Bio-innovation Building, University of Malaga, 29590 Málaga, Spain; Email:<email>rociobm@uma.es</email> (R.B.);<email>dariogf@uma.es</email> (D.G.-F.)</nlm:aff></affiliation></author><author><name sortKey="Seoane, Pedro" sort="Seoane, Pedro" uniqKey="Seoane P" first="Pedro" last="Seoane">Pedro Seoane</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation></author><author><name sortKey="Fernandez Pozo, Noe" sort="Fernandez Pozo, Noe" uniqKey="Fernandez Pozo N" first="Noé" last="Fernández-Pozo">Noé Fernández-Pozo</name><affiliation><nlm:aff id="af1-biology-01-00439">Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Malaga, 29071 Málaga, Spain; Email:<email>bhicham538@gmail.com</email> (H.B.);<email>seoanezonjic@uma.es</email> (P.S.);<email>noefp@uma.es</email> (N.F.-P.)</nlm:aff></affiliation></author></analytic><series><title level="j">Biology</title><idno type="eISSN">2079-7737</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Paterson, A H" uniqKey="Paterson A">A.H. 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Birol</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Bautista, Rocio" sort="Bautista, Rocio" uniqKey="Bautista R" first="Rocío" last="Bautista">Rocío Bautista</name><name sortKey="Benzerki, Hicham" sort="Benzerki, Hicham" uniqKey="Benzerki H" first="Hicham" last="Benzerki">Hicham Benzerki</name><name sortKey="Claros, Manuel Gonzalo" sort="Claros, Manuel Gonzalo" uniqKey="Claros M" first="Manuel Gonzalo" last="Claros">Manuel Gonzalo Claros</name><name sortKey="Fernandez Pozo, Noe" sort="Fernandez Pozo, Noe" uniqKey="Fernandez Pozo N" first="Noé" last="Fernández-Pozo">Noé Fernández-Pozo</name><name sortKey="Guerrero Fernandez, Dario" sort="Guerrero Fernandez, Dario" uniqKey="Guerrero Fernandez D" first="Darío" last="Guerrero-Fernández">Darío Guerrero-Fernández</name><name sortKey="Seoane, Pedro" sort="Seoane, Pedro" uniqKey="Seoane P" first="Pedro" last="Seoane">Pedro Seoane</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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