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A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species

Identifieur interne : 000C07 ( Pmc/Corpus ); précédent : 000C06; suivant : 000C08

A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species

Auteurs : Andres Garcia-Lor ; Franck Curk ; Hager Snoussi-Trifa ; Raphael Morillon ; Gema Ancillo ; François Luro ; Luis Navarro ; Patrick Ollitrault

Source :

Annals of Botany [ 0305-7364 ] ; 2012.

RBID : PMC:3523644

Abstract

Background and Aims

Despite differences in morphology, the genera representing ‘true citrus fruit trees’ are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial ‘species’ of Citrus are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between ‘true citrus fruit trees’ were clarified.

Methods

Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of Citrus and relatives of Citrus to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed.

Key Results

A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that Citrus reticulata and Fortunella form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha). These results confirm the taxonomic subdivision between the subgenera Metacitrus and Archicitrus. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial Citrus spp.

Conclusions

Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for Citrus and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of C. sinensis.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523644

DOI: 10.1093/aob/mcs227
PubMed: 23104641
PubMed Central: 3523644

Links to Exploration step

PMC:3523644

Le document en format XML

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<author><name sortKey="Garcia Lor, Andres" sort="Garcia Lor, Andres" uniqKey="Garcia Lor A" first="Andres" last="Garcia-Lor">Andres Garcia-Lor</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
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<author><name sortKey="Curk, Franck" sort="Curk, Franck" uniqKey="Curk F" first="Franck" last="Curk">Franck Curk</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
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<affiliation><nlm:aff id="af2"><addr-line>INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France</addr-line>
</nlm:aff>
</affiliation>
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<author><name sortKey="Snoussi Trifa, Hager" sort="Snoussi Trifa, Hager" uniqKey="Snoussi Trifa H" first="Hager" last="Snoussi-Trifa">Hager Snoussi-Trifa</name>
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</nlm:aff>
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<author><name sortKey="Morillon, Raphael" sort="Morillon, Raphael" uniqKey="Morillon R" first="Raphael" last="Morillon">Raphael Morillon</name>
<affiliation><nlm:aff id="af4"><addr-line>UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France</addr-line>
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<author><name sortKey="Ancillo, Gema" sort="Ancillo, Gema" uniqKey="Ancillo G" first="Gema" last="Ancillo">Gema Ancillo</name>
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</nlm:aff>
</affiliation>
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<author><name sortKey="Luro, Francois" sort="Luro, Francois" uniqKey="Luro F" first="François" last="Luro">François Luro</name>
<affiliation><nlm:aff id="af2"><addr-line>INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Navarro, Luis" sort="Navarro, Luis" uniqKey="Navarro L" first="Luis" last="Navarro">Luis Navarro</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name>
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</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="af4"><addr-line>UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France</addr-line>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species</title>
<author><name sortKey="Garcia Lor, Andres" sort="Garcia Lor, Andres" uniqKey="Garcia Lor A" first="Andres" last="Garcia-Lor">Andres Garcia-Lor</name>
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</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Curk, Franck" sort="Curk, Franck" uniqKey="Curk F" first="Franck" last="Curk">Franck Curk</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="af2"><addr-line>INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Snoussi Trifa, Hager" sort="Snoussi Trifa, Hager" uniqKey="Snoussi Trifa H" first="Hager" last="Snoussi-Trifa">Hager Snoussi-Trifa</name>
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</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Morillon, Raphael" sort="Morillon, Raphael" uniqKey="Morillon R" first="Raphael" last="Morillon">Raphael Morillon</name>
<affiliation><nlm:aff id="af4"><addr-line>UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ancillo, Gema" sort="Ancillo, Gema" uniqKey="Ancillo G" first="Gema" last="Ancillo">Gema Ancillo</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Luro, Francois" sort="Luro, Francois" uniqKey="Luro F" first="François" last="Luro">François Luro</name>
<affiliation><nlm:aff id="af2"><addr-line>INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Navarro, Luis" sort="Navarro, Luis" uniqKey="Navarro L" first="Luis" last="Navarro">Luis Navarro</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name>
<affiliation><nlm:aff id="af1"><addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="af4"><addr-line>UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France</addr-line>
</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Annals of Botany</title>
<idno type="ISSN">0305-7364</idno>
<idno type="eISSN">1095-8290</idno>
<imprint><date when="2012">2012</date>
</imprint>
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<front><div type="abstract" xml:lang="en"><sec><title>Background and Aims</title>
<p>Despite differences in morphology, the genera representing ‘true citrus fruit trees’ are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial ‘species’ of <italic>Citrus</italic>
 are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between ‘true citrus fruit trees’ were clarified.</p>
</sec>
<sec><title>Methods</title>
<p>Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of <italic>Citrus</italic>
 and relatives of <italic>Citrus</italic>
 to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed.</p>
</sec>
<sec><title>Key Results</title>
<p>A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that <italic>Citrus reticulata</italic>
 and <italic>Fortunella</italic>
 form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (<italic>C. maxima</italic>
, <italic>C. medica</italic>
 and <italic>C. micrantha</italic>
). These results confirm the taxonomic subdivision between the subgenera <italic>Metacitrus</italic>
 and <italic>Archicitrus</italic>
. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial <italic>Citrus</italic>
 spp.</p>
</sec>
<sec><title>Conclusions</title>
<p>Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for <italic>Citrus</italic>
 and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of <italic>C. sinensis</italic>
.</p>
</sec>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Ann Bot</journal-id>
<journal-id journal-id-type="iso-abbrev">Ann. Bot</journal-id>
<journal-id journal-id-type="publisher-id">annbot</journal-id>
<journal-id journal-id-type="hwp">annbot</journal-id>
<journal-title-group><journal-title>Annals of Botany</journal-title>
</journal-title-group>
<issn pub-type="ppub">0305-7364</issn>
<issn pub-type="epub">1095-8290</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23104641</article-id>
<article-id pub-id-type="pmc">3523644</article-id>
<article-id pub-id-type="doi">10.1093/aob/mcs227</article-id>
<article-id pub-id-type="publisher-id">mcs227</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Garcia-Lor</surname>
<given-names>Andres</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Curk</surname>
<given-names>Franck</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
<xref ref-type="aff" rid="af2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Snoussi-Trifa</surname>
<given-names>Hager</given-names>
</name>
<xref ref-type="aff" rid="af3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Morillon</surname>
<given-names>Raphael</given-names>
</name>
<xref ref-type="aff" rid="af4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ancillo</surname>
<given-names>Gema</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Luro</surname>
<given-names>François</given-names>
</name>
<xref ref-type="aff" rid="af2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Navarro</surname>
<given-names>Luis</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ollitrault</surname>
<given-names>Patrick</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
<xref ref-type="aff" rid="af4">4</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
</contrib-group>
<aff id="af1"><label>1</label>
<addr-line>Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain</addr-line>
</aff>
<aff id="af2"><label>2</label>
<addr-line>INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France</addr-line>
</aff>
<aff id="af3"><label>3</label>
<addr-line>Horticultural Laboratory, Tunisian National Agronomic Research Institute (INRAT), Rue Hedi Karray, 2049 Ariana, Tunisia</addr-line>
</aff>
<aff id="af4"><label>4</label>
<addr-line>UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France</addr-line>
</aff>
<author-notes><corresp id="cor1"><label>*</label>
For correspondence. E-mail <email>patrick.ollitrault@cirad.fr</email>
 or <email>lnavarro@ivia.es</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>1</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>26</day>
<month>10</month>
<year>2012</year>
</pub-date>
<volume>111</volume>
<issue>1</issue>
<fpage>1</fpage>
<lpage>19</lpage>
<history><date date-type="received"><day>27</day>
<month>4</month>
<year>2012</year>
</date>
<date date-type="rev-request"><day>23</day>
<month>7</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>12</day>
<month>9</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2012. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com</copyright-statement>
<copyright-year>2012</copyright-year>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="mcs227.pdf"></self-uri>
<abstract><sec><title>Background and Aims</title>
<p>Despite differences in morphology, the genera representing ‘true citrus fruit trees’ are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial ‘species’ of <italic>Citrus</italic>
 are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between ‘true citrus fruit trees’ were clarified.</p>
</sec>
<sec><title>Methods</title>
<p>Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of <italic>Citrus</italic>
 and relatives of <italic>Citrus</italic>
 to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed.</p>
</sec>
<sec><title>Key Results</title>
<p>A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that <italic>Citrus reticulata</italic>
 and <italic>Fortunella</italic>
 form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (<italic>C. maxima</italic>
, <italic>C. medica</italic>
 and <italic>C. micrantha</italic>
). These results confirm the taxonomic subdivision between the subgenera <italic>Metacitrus</italic>
 and <italic>Archicitrus</italic>
. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial <italic>Citrus</italic>
 spp.</p>
</sec>
<sec><title>Conclusions</title>
<p>Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for <italic>Citrus</italic>
 and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of <italic>C. sinensis</italic>
.</p>
</sec>
</abstract>
<kwd-group><kwd>Phylogeny</kwd>
<kwd>evolution</kwd>
<kwd>SNP</kwd>
<kwd>indel</kwd>
<kwd>SSR</kwd>
<kwd>Rutaceae</kwd>
<kwd><italic>Citrus</italic>
</kwd>
<kwd><italic>Fortunella</italic>
</kwd>
<kwd><italic>Microcitrus</italic>
</kwd>
<kwd><italic>Eremocitrus</italic>
</kwd>
<kwd><italic>Poncirus</italic>
</kwd>
</kwd-group>
<counts><page-count count="20"></page-count>
</counts>
</article-meta>
</front>
</pmc>
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A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species

A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species

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Abstract

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