Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s13007-022-00885-z http://hdl.handle.net/11449/240858 |
Resumo: | Background: Illegal logging is a global crisis with significant environmental, economic, and social consequences. Efforts to combat it call for forensic methods to determine species identity, provenance, and individual identification of wood specimens throughout the forest products supply chain. DNA-based methodologies are the only tools with the potential to answer all three questions and the only ones that can be calibrated “non-destructively” by using leaves or other plant tissue and take advantage of publicly available DNA sequence databases. Despite the potential that DNA-based methods represent for wood forensics, low DNA yield from wood remains a limiting factor because, when compared to other plant tissues, wood has few living DNA-containing cells at functional maturity, it often has PCR-inhibiting extractives, and industrial processing of wood degrades DNA. To overcome these limitations, we developed a technique—organellar microcapture—to mechanically isolate intact nuclei and plastids from wood for subsequent DNA extraction, amplification, and sequencing. Results: Here we demonstrate organellar microcapture wherein we remove individual nuclei from parenchyma cells in wood (fresh and aged) and leaves of Carya ovata and Tilia americana, amyloplasts from Carya wood, and chloroplasts from kale (Brassica sp.) leaf midribs. ITS (773 bp), ITS1 (350 bp), ITS2 (450 bp), and rbcL (620 bp) were amplified via polymerase chain reaction, sequenced, and heuristic searches against the NCBI database were used to confirm that recovered DNA corresponded to each taxon. Conclusion: Organellar microcapture, while too labor-intensive for routine extraction of many specimens, successfully recovered intact nuclei from wood samples collected more than sixty-five years ago, plastids from fresh sapwood and leaves, and presents great potential for DNA extraction from recalcitrant plant samples such as tissues rich in secondary metabolites, old specimens (archaeological, herbarium, and xylarium specimens), or trace evidence previously considered too small for analysis. |
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Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidenceNucleus isolationOrganellar microcapturePlastid isolationSingle-cell sequencingWood identificationBackground: Illegal logging is a global crisis with significant environmental, economic, and social consequences. Efforts to combat it call for forensic methods to determine species identity, provenance, and individual identification of wood specimens throughout the forest products supply chain. DNA-based methodologies are the only tools with the potential to answer all three questions and the only ones that can be calibrated “non-destructively” by using leaves or other plant tissue and take advantage of publicly available DNA sequence databases. Despite the potential that DNA-based methods represent for wood forensics, low DNA yield from wood remains a limiting factor because, when compared to other plant tissues, wood has few living DNA-containing cells at functional maturity, it often has PCR-inhibiting extractives, and industrial processing of wood degrades DNA. To overcome these limitations, we developed a technique—organellar microcapture—to mechanically isolate intact nuclei and plastids from wood for subsequent DNA extraction, amplification, and sequencing. Results: Here we demonstrate organellar microcapture wherein we remove individual nuclei from parenchyma cells in wood (fresh and aged) and leaves of Carya ovata and Tilia americana, amyloplasts from Carya wood, and chloroplasts from kale (Brassica sp.) leaf midribs. ITS (773 bp), ITS1 (350 bp), ITS2 (450 bp), and rbcL (620 bp) were amplified via polymerase chain reaction, sequenced, and heuristic searches against the NCBI database were used to confirm that recovered DNA corresponded to each taxon. Conclusion: Organellar microcapture, while too labor-intensive for routine extraction of many specimens, successfully recovered intact nuclei from wood samples collected more than sixty-five years ago, plastids from fresh sapwood and leaves, and presents great potential for DNA extraction from recalcitrant plant samples such as tissues rich in secondary metabolites, old specimens (archaeological, herbarium, and xylarium specimens), or trace evidence previously considered too small for analysis.U.S. Department of StateDepartment of Sustainable Bioproducts Mississippi State UniversityDepartment of Botany University of WisconsinForest Products LaboratoryDepartment of Wood Anatomy and Utilization Chinese Research Institute of Wood Industry Chinese Academy of ForestryWood Collections (WOODPEDIA) Chinese Academy of ForestryDepartment of Forestry and Natural Resources Purdue UniversityDepartamento de Ciências Biológicas (Botânica) Universidade Estadual Paulista–BotucatuDepartamento de Ciências Biológicas (Botânica) Universidade Estadual Paulista–BotucatuU.S. Department of State: 19318814Y0010Mississippi State UniversityUniversity of WisconsinForest Products LaboratoryChinese Academy of ForestryPurdue UniversityUniversidade Estadual Paulista (UNESP)Costa, AdrianaGiraldo, GiovannyBishell, AmyHe, TuoKirker, GrantWiedenhoeft, Alex C. [UNESP]2023-03-01T20:35:52Z2023-03-01T20:35:52Z2022-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s13007-022-00885-zPlant Methods, v. 18, n. 1, 2022.1746-4811http://hdl.handle.net/11449/24085810.1186/s13007-022-00885-z2-s2.0-85128465408Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPlant Methodsinfo:eu-repo/semantics/openAccess2023-03-01T20:35:52Zoai:repositorio.unesp.br:11449/240858Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-03-01T20:35:52Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
title |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
spellingShingle |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence Costa, Adriana Nucleus isolation Organellar microcapture Plastid isolation Single-cell sequencing Wood identification |
title_short |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
title_full |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
title_fullStr |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
title_full_unstemmed |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
title_sort |
Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence |
author |
Costa, Adriana |
author_facet |
Costa, Adriana Giraldo, Giovanny Bishell, Amy He, Tuo Kirker, Grant Wiedenhoeft, Alex C. [UNESP] |
author_role |
author |
author2 |
Giraldo, Giovanny Bishell, Amy He, Tuo Kirker, Grant Wiedenhoeft, Alex C. [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Mississippi State University University of Wisconsin Forest Products Laboratory Chinese Academy of Forestry Purdue University Universidade Estadual Paulista (UNESP) |
dc.contributor.author.fl_str_mv |
Costa, Adriana Giraldo, Giovanny Bishell, Amy He, Tuo Kirker, Grant Wiedenhoeft, Alex C. [UNESP] |
dc.subject.por.fl_str_mv |
Nucleus isolation Organellar microcapture Plastid isolation Single-cell sequencing Wood identification |
topic |
Nucleus isolation Organellar microcapture Plastid isolation Single-cell sequencing Wood identification |
description |
Background: Illegal logging is a global crisis with significant environmental, economic, and social consequences. Efforts to combat it call for forensic methods to determine species identity, provenance, and individual identification of wood specimens throughout the forest products supply chain. DNA-based methodologies are the only tools with the potential to answer all three questions and the only ones that can be calibrated “non-destructively” by using leaves or other plant tissue and take advantage of publicly available DNA sequence databases. Despite the potential that DNA-based methods represent for wood forensics, low DNA yield from wood remains a limiting factor because, when compared to other plant tissues, wood has few living DNA-containing cells at functional maturity, it often has PCR-inhibiting extractives, and industrial processing of wood degrades DNA. To overcome these limitations, we developed a technique—organellar microcapture—to mechanically isolate intact nuclei and plastids from wood for subsequent DNA extraction, amplification, and sequencing. Results: Here we demonstrate organellar microcapture wherein we remove individual nuclei from parenchyma cells in wood (fresh and aged) and leaves of Carya ovata and Tilia americana, amyloplasts from Carya wood, and chloroplasts from kale (Brassica sp.) leaf midribs. ITS (773 bp), ITS1 (350 bp), ITS2 (450 bp), and rbcL (620 bp) were amplified via polymerase chain reaction, sequenced, and heuristic searches against the NCBI database were used to confirm that recovered DNA corresponded to each taxon. Conclusion: Organellar microcapture, while too labor-intensive for routine extraction of many specimens, successfully recovered intact nuclei from wood samples collected more than sixty-five years ago, plastids from fresh sapwood and leaves, and presents great potential for DNA extraction from recalcitrant plant samples such as tissues rich in secondary metabolites, old specimens (archaeological, herbarium, and xylarium specimens), or trace evidence previously considered too small for analysis. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-12-01 2023-03-01T20:35:52Z 2023-03-01T20:35:52Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1186/s13007-022-00885-z Plant Methods, v. 18, n. 1, 2022. 1746-4811 http://hdl.handle.net/11449/240858 10.1186/s13007-022-00885-z 2-s2.0-85128465408 |
url |
http://dx.doi.org/10.1186/s13007-022-00885-z http://hdl.handle.net/11449/240858 |
identifier_str_mv |
Plant Methods, v. 18, n. 1, 2022. 1746-4811 10.1186/s13007-022-00885-z 2-s2.0-85128465408 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Plant Methods |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799965162707353600 |