Regional differences in clonal Japanese knotweed revealed by chemometrics-linked attenuated total reflection Fourier-transform infrared spectroscopy
Background Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this gene...
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| description | Background Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this genetic continuity, Japanese knotweed can colonise a wide variety of environmental habitats. However, little is known about the phenotypic plasticity responsible for the ability of Japanese knotweed to invade and thrive in such diverse habitats. We have used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, in which the spectral fingerprint generated allows subtle differences in composition to be clearly visualized, to examine regional differences in clonal Japanese knotweed. Results We have shown distinct differences in the spectral fingerprint region (1800-900 cm(- 1)) of Japanese knotweed from three different regions in the UK that were sufficient to successfully identify plants from different geographical regions with high accuracy using support vector machine (SVM) chemometrics. Conclusions These differences were not correlated with environmental variations between regions, raising the possibility that epigenetic modifications may contribute to the phenotypic plasticity responsible for the ability of R. japonica to invade and thrive in such diverse habitats. |
| doi_str_mv | 10.1186/s12870-021-03293-y |
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M. ; Taylor, Jane E. ; Martin, Francis L. ; Beckett, Paul ; McAinsh, Martin</creator><creatorcontrib>Holden, Claire A. ; Morais, Camilo L. M. ; Taylor, Jane E. ; Martin, Francis L. ; Beckett, Paul ; McAinsh, Martin</creatorcontrib><description>Background Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this genetic continuity, Japanese knotweed can colonise a wide variety of environmental habitats. However, little is known about the phenotypic plasticity responsible for the ability of Japanese knotweed to invade and thrive in such diverse habitats. We have used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, in which the spectral fingerprint generated allows subtle differences in composition to be clearly visualized, to examine regional differences in clonal Japanese knotweed. Results We have shown distinct differences in the spectral fingerprint region (1800-900 cm(- 1)) of Japanese knotweed from three different regions in the UK that were sufficient to successfully identify plants from different geographical regions with high accuracy using support vector machine (SVM) chemometrics. Conclusions These differences were not correlated with environmental variations between regions, raising the possibility that epigenetic modifications may contribute to the phenotypic plasticity responsible for the ability of R. japonica to invade and thrive in such diverse habitats.</description><identifier>ISSN: 1471-2229</identifier><identifier>EISSN: 1471-2229</identifier><identifier>DOI: 10.1186/s12870-021-03293-y</identifier><identifier>PMID: 34753418</identifier><language>eng</language><publisher>LONDON: Springer Nature</publisher><subject>Adaptation, Physiological - genetics ; Analysis ; Carotenoids ; Chemometrics ; Climate ; Crop damage ; Crop losses ; Discriminant analysis ; Ecosystem ; Ecosystem services ; Environment ; Epigenetics ; Epigenomics ; Fallopia japonica - chemistry ; Fallopia japonica - genetics ; Fallopia japonica - growth & development ; Fingerprints ; Fourier transforms ; FTIR spectroscopy ; Genetic aspects ; Genetic diversity ; Growth ; Habitats ; Identification and classification ; Infrared reflection ; Infrared spectroscopy ; Introduced Species ; Invasive species ; Japanese knotweed ; Life Sciences & Biomedicine ; Lignin ; Methods ; Neural networks ; Phenotypic plasticity ; Phylogeography ; Physiological adaptation ; Plant Sciences ; Plastic properties ; Plasticity ; Polygonaceae ; Polygonum ; Regional differences ; Regions ; Reproduction (biology) ; Science & Technology ; Soil ; Spectroscopy, Fourier Transform Infrared ; Spectrum analysis ; Support vector machines ; Vegetative reproduction</subject><ispartof>BMC plant biology, 2021-11, Vol.21 (1), p.522-522, Article 522</ispartof><rights>2021. The Author(s).</rights><rights>COPYRIGHT 2021 BioMed Central Ltd.</rights><rights>2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>8</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000716448400001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c597t-b972b20ca5b5e448e3dd37248dfed5d8df195f493c8f38690de0b3a9ad7aa0933</citedby><cites>FETCH-LOGICAL-c597t-b972b20ca5b5e448e3dd37248dfed5d8df195f493c8f38690de0b3a9ad7aa0933</cites><orcidid>0000-0002-7831-8671 ; 0000-0002-1467-7149 ; 0000-0003-4294-6470 ; 0000-0003-2573-787X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8579538/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8579538/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,866,887,2106,2118,27933,27934,39267,53800,53802</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34753418$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Holden, Claire A.</creatorcontrib><creatorcontrib>Morais, Camilo L. M.</creatorcontrib><creatorcontrib>Taylor, Jane E.</creatorcontrib><creatorcontrib>Martin, Francis L.</creatorcontrib><creatorcontrib>Beckett, Paul</creatorcontrib><creatorcontrib>McAinsh, Martin</creatorcontrib><title>Regional differences in clonal Japanese knotweed revealed by chemometrics-linked attenuated total reflection Fourier-transform infrared spectroscopy</title><title>BMC plant biology</title><addtitle>BMC PLANT BIOL</addtitle><addtitle>BMC Plant Biol</addtitle><description>Background Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this genetic continuity, Japanese knotweed can colonise a wide variety of environmental habitats. However, little is known about the phenotypic plasticity responsible for the ability of Japanese knotweed to invade and thrive in such diverse habitats. We have used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, in which the spectral fingerprint generated allows subtle differences in composition to be clearly visualized, to examine regional differences in clonal Japanese knotweed. Results We have shown distinct differences in the spectral fingerprint region (1800-900 cm(- 1)) of Japanese knotweed from three different regions in the UK that were sufficient to successfully identify plants from different geographical regions with high accuracy using support vector machine (SVM) chemometrics. Conclusions These differences were not correlated with environmental variations between regions, raising the possibility that epigenetic modifications may contribute to the phenotypic plasticity responsible for the ability of R. japonica to invade and thrive in such diverse habitats.</description><subject>Adaptation, Physiological - genetics</subject><subject>Analysis</subject><subject>Carotenoids</subject><subject>Chemometrics</subject><subject>Climate</subject><subject>Crop damage</subject><subject>Crop losses</subject><subject>Discriminant analysis</subject><subject>Ecosystem</subject><subject>Ecosystem services</subject><subject>Environment</subject><subject>Epigenetics</subject><subject>Epigenomics</subject><subject>Fallopia japonica - chemistry</subject><subject>Fallopia japonica - genetics</subject><subject>Fallopia japonica - growth & development</subject><subject>Fingerprints</subject><subject>Fourier transforms</subject><subject>FTIR spectroscopy</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Growth</subject><subject>Habitats</subject><subject>Identification and classification</subject><subject>Infrared reflection</subject><subject>Infrared spectroscopy</subject><subject>Introduced Species</subject><subject>Invasive species</subject><subject>Japanese knotweed</subject><subject>Life Sciences & Biomedicine</subject><subject>Lignin</subject><subject>Methods</subject><subject>Neural networks</subject><subject>Phenotypic plasticity</subject><subject>Phylogeography</subject><subject>Physiological adaptation</subject><subject>Plant Sciences</subject><subject>Plastic properties</subject><subject>Plasticity</subject><subject>Polygonaceae</subject><subject>Polygonum</subject><subject>Regional differences</subject><subject>Regions</subject><subject>Reproduction (biology)</subject><subject>Science & Technology</subject><subject>Soil</subject><subject>Spectroscopy, Fourier Transform Infrared</subject><subject>Spectrum analysis</subject><subject>Support vector machines</subject><subject>Vegetative reproduction</subject><issn>1471-2229</issn><issn>1471-2229</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>HGBXW</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNksFu1DAQhiMEoqXwAhxQJC4glGLHSWxfkKoVhUWVkAqcLceebL1N4sV2WvY9eGBmd8vSRRxQDh5Nvvkt__Nn2XNKTikVzdtIS8FJQUpaEFZKVqwfZMe04rQoy1I-vFcfZU9iXBJCuajk4-yIVbxmFRXH2c9LWDg_6j63rusgwGgg5m7MTb_tftIrPUKE_Hr06RbA5gFuQPdYtOvcXMHgB0jBmVj0brzGtk4JxkknLJNPKBGg68EkvCU_91NwEIoU9Bg7Hwa8qQs6IBtXyAQfjV-tn2aPOt1HeHZ3nmTfzt9_nX0sLj5_mM_OLgpTS56KVvKyLYnRdVtDVQlg1jJeVsJ2YGuLB5V1V0lmRMdEI4kF0jItteVaE8nYSTbf6Vqvl2oV3KDDWnnt1Lbhw0LpkJzpQZWmxTFmJWhbWWuFJMB5A5oxTq1uUOvdTms1tQNYAyM-sj8QPfwzuiu18DdK1FzWTKDAqzuB4L9PEJMaXDTQ9-i_n6Iqa9kQimvboC__QpdoLK5rS0kqS8L4H2qB61JotMd7zUZUnTWiqVhDmo0Hp_-g8LMwOONH6Bz2DwZeHwwgk-BHWugpRjX_cnnIljvW4GYjBmHvByVqk2G1y7DCDKtthtUah17cd3I_8ju0CLzZAbfQ-i4atwntHiOEcNpgHCqsCEVa_D89c0lvkjrz05jYL84BEUc</recordid><startdate>20211109</startdate><enddate>20211109</enddate><creator>Holden, Claire A.</creator><creator>Morais, Camilo L. 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M. ; Taylor, Jane E. ; Martin, Francis L. ; Beckett, Paul ; McAinsh, Martin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c597t-b972b20ca5b5e448e3dd37248dfed5d8df195f493c8f38690de0b3a9ad7aa0933</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Adaptation, Physiological - genetics</topic><topic>Analysis</topic><topic>Carotenoids</topic><topic>Chemometrics</topic><topic>Climate</topic><topic>Crop damage</topic><topic>Crop losses</topic><topic>Discriminant analysis</topic><topic>Ecosystem</topic><topic>Ecosystem services</topic><topic>Environment</topic><topic>Epigenetics</topic><topic>Epigenomics</topic><topic>Fallopia japonica - chemistry</topic><topic>Fallopia japonica - genetics</topic><topic>Fallopia japonica - growth & development</topic><topic>Fingerprints</topic><topic>Fourier transforms</topic><topic>FTIR spectroscopy</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Growth</topic><topic>Habitats</topic><topic>Identification and classification</topic><topic>Infrared reflection</topic><topic>Infrared spectroscopy</topic><topic>Introduced Species</topic><topic>Invasive species</topic><topic>Japanese knotweed</topic><topic>Life Sciences & Biomedicine</topic><topic>Lignin</topic><topic>Methods</topic><topic>Neural networks</topic><topic>Phenotypic plasticity</topic><topic>Phylogeography</topic><topic>Physiological adaptation</topic><topic>Plant Sciences</topic><topic>Plastic properties</topic><topic>Plasticity</topic><topic>Polygonaceae</topic><topic>Polygonum</topic><topic>Regional differences</topic><topic>Regions</topic><topic>Reproduction (biology)</topic><topic>Science & Technology</topic><topic>Soil</topic><topic>Spectroscopy, Fourier Transform Infrared</topic><topic>Spectrum analysis</topic><topic>Support vector machines</topic><topic>Vegetative reproduction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Holden, Claire A.</creatorcontrib><creatorcontrib>Morais, Camilo L. 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M.</au><au>Taylor, Jane E.</au><au>Martin, Francis L.</au><au>Beckett, Paul</au><au>McAinsh, Martin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Regional differences in clonal Japanese knotweed revealed by chemometrics-linked attenuated total reflection Fourier-transform infrared spectroscopy</atitle><jtitle>BMC plant biology</jtitle><stitle>BMC PLANT BIOL</stitle><addtitle>BMC Plant Biol</addtitle><date>2021-11-09</date><risdate>2021</risdate><volume>21</volume><issue>1</issue><spage>522</spage><epage>522</epage><pages>522-522</pages><artnum>522</artnum><issn>1471-2229</issn><eissn>1471-2229</eissn><abstract>Background Japanese knotweed (R. japonica var japonica) is one of the world's 100 worst invasive species, causing crop losses, damage to infrastructure, and erosion of ecosystem services. In the UK, this species is an all-female clone, which spreads by vegetative reproduction. Despite this genetic continuity, Japanese knotweed can colonise a wide variety of environmental habitats. However, little is known about the phenotypic plasticity responsible for the ability of Japanese knotweed to invade and thrive in such diverse habitats. We have used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, in which the spectral fingerprint generated allows subtle differences in composition to be clearly visualized, to examine regional differences in clonal Japanese knotweed. Results We have shown distinct differences in the spectral fingerprint region (1800-900 cm(- 1)) of Japanese knotweed from three different regions in the UK that were sufficient to successfully identify plants from different geographical regions with high accuracy using support vector machine (SVM) chemometrics. Conclusions These differences were not correlated with environmental variations between regions, raising the possibility that epigenetic modifications may contribute to the phenotypic plasticity responsible for the ability of R. japonica to invade and thrive in such diverse habitats.</abstract><cop>LONDON</cop><pub>Springer Nature</pub><pmid>34753418</pmid><doi>10.1186/s12870-021-03293-y</doi><tpages>20</tpages><orcidid>https://orcid.org/0000-0002-7831-8671</orcidid><orcidid>https://orcid.org/0000-0002-1467-7149</orcidid><orcidid>https://orcid.org/0000-0003-4294-6470</orcidid><orcidid>https://orcid.org/0000-0003-2573-787X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Adaptation, Physiological - genetics Analysis Carotenoids Chemometrics Climate Crop damage Crop losses Discriminant analysis Ecosystem Ecosystem services Environment Epigenetics Epigenomics Fallopia japonica - chemistry Fallopia japonica - genetics Fallopia japonica - growth & development Fingerprints Fourier transforms FTIR spectroscopy Genetic aspects Genetic diversity Growth Habitats Identification and classification Infrared reflection Infrared spectroscopy Introduced Species Invasive species Japanese knotweed Life Sciences & Biomedicine Lignin Methods Neural networks Phenotypic plasticity Phylogeography Physiological adaptation Plant Sciences Plastic properties Plasticity Polygonaceae Polygonum Regional differences Regions Reproduction (biology) Science & Technology Soil Spectroscopy, Fourier Transform Infrared Spectrum analysis Support vector machines Vegetative reproduction |
| title | Regional differences in clonal Japanese knotweed revealed by chemometrics-linked attenuated total reflection Fourier-transform infrared spectroscopy |
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