Whole-chloroplast phylogenomics
Definition
Using complete chloroplast genome sequences (plastomes, ~120-160 kb) to reconstruct phylogenetic relationships and assign an unknown plant to a geographic clade or maternal lineage with far more resolution than two-locus barcoding.
Related terms
- Environmental DNA (eDNA)
- DNA extracted from an environmental matrix (soil, water, air filter) rather than from a discrete specimen. For plant forensics, eDNA metabarcoding generates...
- Metabarcoding
- High-throughput sequencing of a barcode locus from a bulk environmental or mixture sample, identifying all taxa present from a reference database. Used...
- Microsatellite (SSR) profiling
- Detection of variation at short tandem repeat loci in the nuclear genome. SSR loci are codominant, highly polymorphic, and reproducible across labs....
- Next-generation sequencing (NGS)
- High-throughput sequencing technologies (Illumina, Ion Torrent, Oxford Nanopore) that produce millions of reads in parallel. For plant forensics, they enable whole-chloroplast genome...
- Validation (forensic method)
- The process of demonstrating that a method is fit for its intended forensic purpose: reproducibility, sensitivity, specificity, and performance on simulated casework...
Explained in
- Emerging Plant Genomics in CaseworkUsing complete chloroplast genome sequences (plastomes, ~120-160 kb) to reconstruct phylogenetic relationships and assign an unknown plant to a geographic clad...