The American cranberry: first insights into the whole genome of a species adapted to bog habitat
Identifieur interne : 000B49 ( Pmc/Curation ); précédent : 000B48; suivant : 000B50The American cranberry: first insights into the whole genome of a species adapted to bog habitat
Auteurs : James Polashock [États-Unis] ; Ehud Zelzion [États-Unis] ; Diego Fajardo [États-Unis] ; Juan Zalapa [États-Unis] ; Laura Georgi [États-Unis] ; Debashish Bhattacharya [États-Unis] ; Nicholi Vorsa [États-Unis]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2014.
Abstract
The American cranberry (
The genome size of
Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.
Url:
DOI: 10.1186/1471-2229-14-165
PubMed: 24927653
PubMed Central: 4076063
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The American cranberry: first insights into the whole genome of a species adapted to bog habitat</title>
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<wicri:regionArea>P.E. Marucci Center for Blueberry and Cranberry Research, 125A Lake Oswego Rd., Chatsworth, New Jersey 08019</wicri:regionArea>
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<series><title level="j">BMC Plant Biology</title>
<idno type="eISSN">1471-2229</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The American cranberry (<italic>Vaccinium macrocarpon</italic>
Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (<italic>Vaccinium</italic>
spp.) and native grape (<italic>Vitis</italic>
spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2<italic>n</italic>
= 2<italic>x</italic>
= 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.</p>
</sec>
<sec><title>Results</title>
<p>The genome size of <italic>V. macrocarpon</italic>
has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).</p>
</sec>
<sec><title>Conclusions</title>
<p>Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Plant Biol</journal-id>
<journal-title-group><journal-title>BMC Plant Biology</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2229</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24927653</article-id>
<article-id pub-id-type="pmc">4076063</article-id>
<article-id pub-id-type="publisher-id">1471-2229-14-165</article-id>
<article-id pub-id-type="doi">10.1186/1471-2229-14-165</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>The American cranberry: first insights into the whole genome of a species adapted to bog habitat</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Polashock</surname>
<given-names>James</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>James.Polashock@ars.usda.gov</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Zelzion</surname>
<given-names>Ehud</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>udizel@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Fajardo</surname>
<given-names>Diego</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>dfajar2@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Zalapa</surname>
<given-names>Juan</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>Juan.Zalapa@ars.usda.gov</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Georgi</surname>
<given-names>Laura</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
<xref ref-type="aff" rid="I6">6</xref>
<email>laura@acf.org</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Bhattacharya</surname>
<given-names>Debashish</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Bhattacharya@aesop.rutgers.edu</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Vorsa</surname>
<given-names>Nicholi</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>Vorsa@aesop.rutgers.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
USDA, Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Lab, 125A Lake Oswego Rd., Chatsworth, New Jersey 08019, USA</aff>
<aff id="I2"><label>2</label>
Department of Ecology, Evolution and Natural Resources, Rutgers University, 59 Dudley Rd., New Brunswick, New Jersey 08901, USA</aff>
<aff id="I3"><label>3</label>
Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706, USA</aff>
<aff id="I4"><label>4</label>
USDA, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin 53706, USA</aff>
<aff id="I5"><label>5</label>
P.E. Marucci Center for Blueberry and Cranberry Research, 125A Lake Oswego Rd., Chatsworth, New Jersey 08019, USA</aff>
<aff id="I6"><label>6</label>
Current address: American Chestnut Foundation, Meadowview Research Farms, 29010, Hawthorne, Dr., Meadowview, Virginia 24361, USA</aff>
<aff id="I7"><label>7</label>
Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ 08901, USA</aff>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>6</month>
<year>2014</year>
</pub-date>
<volume>14</volume>
<fpage>165</fpage>
<lpage>165</lpage>
<history><date date-type="received"><day>7</day>
<month>1</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>3</day>
<month>6</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Polashock et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>Polashock et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2229/14/165"></self-uri>
<abstract><sec><title>Background</title>
<p>The American cranberry (<italic>Vaccinium macrocarpon</italic>
Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (<italic>Vaccinium</italic>
spp.) and native grape (<italic>Vitis</italic>
spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2<italic>n</italic>
= 2<italic>x</italic>
= 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.</p>
</sec>
<sec><title>Results</title>
<p>The genome size of <italic>V. macrocarpon</italic>
has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).</p>
</sec>
<sec><title>Conclusions</title>
<p>Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.</p>
</sec>
</abstract>
<kwd-group><kwd><italic>Vaccinium macrocarpon</italic>
</kwd>
<kwd>Ericaceae</kwd>
<kwd>Transcriptome</kwd>
<kwd>COSII</kwd>
<kwd>Polyphenolics</kwd>
<kwd>Resistance genes</kwd>
<kwd>SSRs</kwd>
<kwd>SNPs</kwd>
<kwd>Inbred</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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