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
- Sequencing a mixture of DNA from many organisms simultaneously and using bioinformatics to assign each read to a taxon. For plant eDNA,...
- 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...