Why Assembling Plant Genome Sequences Is So Challenging
Identifieur interne : 000362 ( Pmc/Checkpoint ); précédent : 000361; suivant : 000363Why 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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PMC:4009782Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Why Assembling Plant Genome Sequences Is So Challenging</title>
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<author><name sortKey="Bautista, Rocio" sort="Bautista, Rocio" uniqKey="Bautista R" first="Rocío" last="Bautista">Rocío Bautista</name>
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<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>
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</back>
</TEI>
<pmc article-type="review-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Biology (Basel)</journal-id>
<journal-id journal-id-type="iso-abbrev">Biology (Basel)</journal-id>
<journal-id journal-id-type="publisher-id">biology</journal-id>
<journal-title-group><journal-title>Biology</journal-title>
</journal-title-group>
<issn pub-type="epub">2079-7737</issn>
<publisher><publisher-name>MDPI</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24832233</article-id>
<article-id pub-id-type="pmc">4009782</article-id>
<article-id pub-id-type="doi">10.3390/biology1020439</article-id>
<article-id pub-id-type="publisher-id">biology-01-00439</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Review</subject>
</subj-group>
</article-categories>
<title-group><article-title>Why Assembling Plant Genome Sequences Is So Challenging</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Claros</surname>
<given-names>Manuel Gonzalo</given-names>
</name>
<xref ref-type="aff" rid="af1-biology-01-00439">1</xref>
<xref ref-type="aff" rid="af2-biology-01-00439">2</xref>
<xref rid="c1-biology-01-00439" ref-type="corresp">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bautista</surname>
<given-names>Rocío</given-names>
</name>
<xref ref-type="aff" rid="af2-biology-01-00439">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Guerrero-Fernández</surname>
<given-names>Darío</given-names>
</name>
<xref ref-type="aff" rid="af2-biology-01-00439">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Benzerki</surname>
<given-names>Hicham</given-names>
</name>
<xref ref-type="aff" rid="af1-biology-01-00439">1</xref>
<xref ref-type="aff" rid="af2-biology-01-00439">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Seoane</surname>
<given-names>Pedro</given-names>
</name>
<xref ref-type="aff" rid="af1-biology-01-00439">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fernández-Pozo</surname>
<given-names>Noé</given-names>
</name>
<xref ref-type="aff" rid="af1-biology-01-00439">1</xref>
</contrib>
</contrib-group>
<aff id="af1-biology-01-00439"><label>1</label>
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.)</aff>
<aff id="af2-biology-01-00439"><label>2</label>
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.)</aff>
<author-notes><corresp id="c1-biology-01-00439"><label>*</label>
Author to whom correspondence should be addressed; Email: <email>claros@uma.es</email>
; Tel.: +34-951-952-787; Fax: +34-952-132-041.</corresp>
</author-notes>
<pub-date pub-type="epub"><day>18</day>
<month>9</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="collection"><month>9</month>
<year>2012</year>
</pub-date>
<volume>1</volume>
<issue>2</issue>
<fpage>439</fpage>
<lpage>459</lpage>
<history><date date-type="received"><day>16</day>
<month>7</month>
<year>2012</year>
</date>
<date date-type="rev-recd"><day>05</day>
<month>9</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>06</day>
<month>9</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>© 2012 by the authors; licensee MDPI, Basel, Switzerland.</copyright-statement>
<copyright-year>2012</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>
).</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<kwd-group><kwd>plant sequencing</kwd>
<kwd>NGS</kwd>
<kwd>complexity</kwd>
<kwd>repeats</kwd>
<kwd>assemblers</kwd>
<kwd>polyploidy</kwd>
<kwd>bioinformatics</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<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>
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