Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence

• Published in: Plant methods Vol. 18; no. 1; p. 51
• Main Authors: Costa, Adriana, Giraldo, Giovanny, Bishell, Amy, He, Tuo, Kirker, Grant, Wiedenhoeft, Alex C
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 20.04.2022; BioMed Central; BMC
• Subjects: Amplification; Analysis; Archaeology; Brassica; Carya ovata; Chemical properties; Chloroplasts; Deoxyribonucleic acid; DNA; DNA sequencing; Endangered & extinct species; Forensic science; Forest products; Genetic aspects; Identification; Leaves; Logging; Metabolites; Methodology; Methods; Nuclei; Nuclei (cytology); Nucleotide sequence; Nucleus isolation; Organellar microcapture; Parenchyma; Parenchyma (Botany); Plant tissues; Plants; Plastid isolation; Plastids; Polymerase chain reaction; Secondary metabolites; Single-cell sequencing; Supply chains; Tilia americana; Wood; Wood identification; Brazil; Nucleus isolation; Single-cell sequencing; Wood identification; Organellar microcapture; Plastid isolation
• ISSN: 1746-4811; 1746-4811
• DOI: 10.1186/s13007-022-00885-z

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. 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. 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.