Plastid Genome Evolution in Parasitic Plants

Plastid genomes in parasitic plants reveal a striking departure from the conserved architecture found in autotrophic lineages. As plants shift to partial or complete heterotrophy, selective pressures on photosynthesis-related genes relax, leading to sequential gene loss, structural rearrangements and genome condensation. Early stages of parasitism often coincide with loss or pseudogenisation of the NADH dehydrogenase (ndh) gene complex, whereas more advanced holoparasites exhibit wholesale elimination of photosystem and RuBisCO genes. Intergenic regions contract, inverted repeats may be reduced or lost, and nucleotide composition can become highly biased. Occasionally, horizontal transfers of plastid fragments to mitochondrial genomes or between host and parasite further complicate plastome trajectories. Despite extensive reduction, retention of a core suite of housekeeping and tRNA genes under purifying selection underscores the essential roles of plastid translational and metabolic functions, even in non-photosynthetic species.

Research from Nature Portfolio

Recent work on hemiparasitic mistletoes has uncovered parallel gene losses and structural deletions affecting small single-copy regions. Complete chloroplast sequencing of two Taxillus species demonstrated the coordinated loss of all ndh genes alongside several ribosomal and ycf genes, resulting in plastomes reduced by over 20 percent. Comparative analyses revealed differing patterns of gene retention and pseudogenisation between Illumina and long-read assemblies, emphasising the impact of sequencing technology on genome reconstruction. Phylogenetic placement confirmed monophyly of major mistletoe clades and highlighted how plastome degeneration correlates with host dependency.

Plastid Genome Evolution in Parasitic Plants publication trend

The graph below shows the total number of articles in plastid genome evolution in parasitic plants across all publications each year (not limited to Nature Index journals).

Technical terms

Plastome: The circular DNA genome of a plastid, encoding photosynthetic and housekeeping genes.

ndh genes: A set of plastid-encoded genes for NADH dehydrogenase subunits involved in photosynthetic electron transport and stress protection.

Inverted repeat (IR): Two identical or nearly identical sequences in opposite orientation that separate single-copy regions in plastid genomes.

Holoparasitic and hemiparasitic: Holoparasites lack photosynthesis entirely and depend wholly on a host, whereas hemiparasites retain some photosynthetic capacity.

Horizontal gene transfer (HGT): The movement of genetic material between distinct genomes, often seen as plastid sequences inserted into mitochondrial DNA or acquired from host plants.

References

1. Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. Scientific Reports (2017).
2. Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae). International Journal of Molecular Sciences (2023).
3. Extreme plastomes in holoparasitic Balanophoraceae are not the norm. BMC Genomics (2023).
4. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biology (2007).