RustFungiGenomicsV1, Main, Exploration, bibRecord, 000055

Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.

Identifieur interne : 000055 ( Main/Exploration ); précédent : 000054; suivant : 000056

Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.

Auteurs : Giovanni Cafa [Royaume-Uni] ; Riccardo Baroncelli [Espagne] ; Carol A. Ellison [Royaume-Uni] ; Daisuke Kurose [Royaume-Uni]

Source :

PeerJ [ 2167-8359 ] ; 2020.

RBID : pubmed:32231875

Abstract

Background

Himalayan balsam

Methods

In this molecular study, two new complete chloroplast (cp) genomes of

Results

The complete cp genomes were double-stranded molecules of 152,260 bp (HB92) and 152,203 bp (HB10) in length and showed 97 variable sites: 27 intragenic and 70 intergenic. The two genomes were aligned and mapped with two closely related genomes used as references. Genome skimming generates complete organellar genomes with limited technical and financial efforts and produces large datasets compared to multi-locus sequence typing. This study demonstrates the suitability of genome skimming for generating complete cp genomes of historic herbarium material. It also shows that complete cp genomes are solid genetic markers for population studies that could be linked to plant evolution and aid with targeting native range and natural enemy surveys for biocontrol of invasive species.

DOI: 10.7717/peerj.8739
PubMed: 32231875
PubMed Central: PMC7100601

Affiliations:

Espagne, Royaume-Uni

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 (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.</title>
<author><name sortKey="Cafa, Giovanni" sort="Cafa, Giovanni" uniqKey="Cafa G" first="Giovanni" last="Cafa">Giovanni Cafa</name>
<affiliation wicri:level="1"><nlm:affiliation>CABI Europe, Egham, Surrey, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>CABI Europe, Egham, Surrey</wicri:regionArea>
<wicri:noRegion>Surrey</wicri:noRegion>
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</author>
<author><name sortKey="Baroncelli, Riccardo" sort="Baroncelli, Riccardo" uniqKey="Baroncelli R" first="Riccardo" last="Baroncelli">Riccardo Baroncelli</name>
<affiliation wicri:level="1"><nlm:affiliation>University of Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor (Salamanca), Spain.</nlm:affiliation>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>University of Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor (Salamanca)</wicri:regionArea>
<wicri:noRegion>Villamayor (Salamanca)</wicri:noRegion>
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<author><name sortKey="Ellison, Carol A" sort="Ellison, Carol A" uniqKey="Ellison C" first="Carol A" last="Ellison">Carol A. Ellison</name>
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<author><name sortKey="Kurose, Daisuke" sort="Kurose, Daisuke" uniqKey="Kurose D" first="Daisuke" last="Kurose">Daisuke Kurose</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en"><i>Impatiens glandulifera</i>
 (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.</title>
<author><name sortKey="Cafa, Giovanni" sort="Cafa, Giovanni" uniqKey="Cafa G" first="Giovanni" last="Cafa">Giovanni Cafa</name>
<affiliation wicri:level="1"><nlm:affiliation>CABI Europe, Egham, Surrey, UK.</nlm:affiliation>
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<affiliation wicri:level="1"><nlm:affiliation>University of Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor (Salamanca), Spain.</nlm:affiliation>
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<author><name sortKey="Ellison, Carol A" sort="Ellison, Carol A" uniqKey="Ellison C" first="Carol A" last="Ellison">Carol A. Ellison</name>
<affiliation wicri:level="1"><nlm:affiliation>CABI Europe, Egham, Surrey, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
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<wicri:noRegion>Surrey</wicri:noRegion>
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<author><name sortKey="Kurose, Daisuke" sort="Kurose, Daisuke" uniqKey="Kurose D" first="Daisuke" last="Kurose">Daisuke Kurose</name>
<affiliation wicri:level="1"><nlm:affiliation>CABI Europe, Egham, Surrey, UK.</nlm:affiliation>
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<front><div type="abstract" xml:lang="en"><p><b>Background</b>
</p>
<p>Himalayan balsam </p>
</div>
<div type="abstract" xml:lang="en"><p><b>Methods</b>
</p>
<p>In this molecular study, two new complete chloroplast (cp) genomes of </p>
</div>
<div type="abstract" xml:lang="en"><p><b>Results</b>
</p>
<p>The complete cp genomes were double-stranded molecules of 152,260 bp (HB92) and 152,203 bp (HB10) in length and showed 97 variable sites: 27 intragenic and 70 intergenic. The two genomes were aligned and mapped with two closely related genomes used as references. Genome skimming generates complete organellar genomes with limited technical and financial efforts and produces large datasets compared to multi-locus sequence typing. This study demonstrates the suitability of genome skimming for generating complete cp genomes of historic herbarium material. It also shows that complete cp genomes are solid genetic markers for population studies that could be linked to plant evolution and aid with targeting native range and natural enemy surveys for biocontrol of invasive species.</p>
</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32231875</PMID>
<DateRevised><Year>2020</Year>
<Month>09</Month>
<Day>28</Day>
</DateRevised>
<Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN>
<JournalIssue CitedMedium="Print"><Volume>8</Volume>
<PubDate><Year>2020</Year>
</PubDate>
</JournalIssue>
<Title>PeerJ</Title>
<ISOAbbreviation>PeerJ</ISOAbbreviation>
</Journal>
<ArticleTitle><i>Impatiens glandulifera</i>
 (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.</ArticleTitle>
<Pagination><MedlinePgn>e8739</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.8739</ELocationID>
<Abstract><AbstractText Label="Background" NlmCategory="UNASSIGNED">Himalayan balsam <i>Impatiens glandulifera</i>
 Royle (Balsaminaceae) is a highly invasive annual species native of the Himalayas. Biocontrol of the plant using the rust fungus <i>Puccinia komarovii</i>
 var. <i>glanduliferae</i>
 is currently being implemented, but issues have arisen with matching UK weed genotypes with compatible strains of the pathogen. To support successful biocontrol, a better understanding of the host weed population, including potential sources of introductions, of Himalayan balsam is required.</AbstractText>
<AbstractText Label="Methods" NlmCategory="UNASSIGNED">In this molecular study, two new complete chloroplast (cp) genomes of <i>I. glandulifera</i>
 were obtained with low coverage whole genome sequencing (genome skimming). A 125-year-old herbarium specimen (HB92) collected from the native range was sequenced and assembled and compared with a 2-year-old specimen from UK field plants (HB10).</AbstractText>
<AbstractText Label="Results" NlmCategory="UNASSIGNED">The complete cp genomes were double-stranded molecules of 152,260 bp (HB92) and 152,203 bp (HB10) in length and showed 97 variable sites: 27 intragenic and 70 intergenic. The two genomes were aligned and mapped with two closely related genomes used as references. Genome skimming generates complete organellar genomes with limited technical and financial efforts and produces large datasets compared to multi-locus sequence typing. This study demonstrates the suitability of genome skimming for generating complete cp genomes of historic herbarium material. It also shows that complete cp genomes are solid genetic markers for population studies that could be linked to plant evolution and aid with targeting native range and natural enemy surveys for biocontrol of invasive species.</AbstractText>
<CopyrightInformation>© 2020 Cafa et al.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cafa</LastName>
<ForeName>Giovanni</ForeName>
<Initials>G</Initials>
<AffiliationInfo><Affiliation>CABI Europe, Egham, Surrey, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Baroncelli</LastName>
<ForeName>Riccardo</ForeName>
<Initials>R</Initials>
<Identifier Source="ORCID">0000-0002-5878-1159</Identifier>
<AffiliationInfo><Affiliation>University of Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor (Salamanca), Spain.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ellison</LastName>
<ForeName>Carol A</ForeName>
<Initials>CA</Initials>
<AffiliationInfo><Affiliation>CABI Europe, Egham, Surrey, UK.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kurose</LastName>
<ForeName>Daisuke</ForeName>
<Initials>D</Initials>
<Identifier Source="ORCID">0000-0002-8356-4930</Identifier>
<AffiliationInfo><Affiliation>CABI Europe, Egham, Surrey, UK.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2020</Year>
<Month>03</Month>
<Day>24</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>PeerJ</MedlineTA>
<NlmUniqueID>101603425</NlmUniqueID>
<ISSNLinking>2167-8359</ISSNLinking>
</MedlineJournalInfo>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Balsaminaceae</Keyword>
<Keyword MajorTopicYN="N">Chloroplast genome</Keyword>
<Keyword MajorTopicYN="N">Genome skimming</Keyword>
<Keyword MajorTopicYN="N">Impatiens glandulifera</Keyword>
<Keyword MajorTopicYN="N">Phylogenetic analyses</Keyword>
<Keyword MajorTopicYN="N">Whole genome sequencing</Keyword>
</KeywordList>
<CoiStatement>The authors declare that they have no competing interests.</CoiStatement>
</MedlineCitation>
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<Month>07</Month>
<Day>26</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2020</Year>
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<Day>12</Day>
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Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.

Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies.

Source :

Abstract

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