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.
- Target
- Complete chloroplast genome (plastome)
- Typical plastome size
- Roughly 120 to 160 kilobases
- Advantage over barcoding
- Far higher resolution than two-locus methods
- Application
- Geographic clade or maternal lineage assignment
Common questions
Why does whole-chloroplast phylogenomics outperform standard DNA barcoding in plant forensic casework?+
Standard barcoding relies on one or two short marker regions, which may not differ enough between closely related populations, while the full plastome supplies many more variable sites, allowing finer geographic or lineage resolution for an unknown plant sample.
What limits the routine use of whole-chloroplast phylogenomics in casework?+
It requires higher-quality DNA, more sequencing throughput, and reference plastome databases for comparison, so it is generally reserved for cases where standard barcoding cannot resolve the question and the sample quality supports the deeper sequencing effort.
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...