Chloroplast Genome Evolution in Orchidaceae

Chloroplast genomes in the orchid family exhibit a conserved quadripartite structure comprising two inverted repeats (IRs) flanking a large single-copy (LSC) and a small single-copy (SSC) region. Across diverse subfamilies, genome size varies from ca. 19 kb in mycoheterotrophic taxa to c. 178 kb in species with expanded non-coding regions. Frequent losses or pseudogenisation of ndh genes, which encode subunits of the NAD(P)H dehydrogenase complex, have occurred independently in multiple lineages, often accompanied by shifts in IR/SSC boundaries. Intron and gene losses correlate with transitions to heterotrophy, while IR expansion and SSC contraction are evident in several genera. Comparative analyses reveal hypervariable intergenic and coding regions that serve as molecular markers for phylogenetic reconstruction. Plastome rearrangements and variations in substitution rates, particularly in clpP and photosystem genes, illuminate adaptive evolution to diverse ecological niches. The growing wealth of complete plastome sequences has refined the phylogenetic framework of Orchidaceae, resolving relationships among subfamilies and tribes and informing conservation and breeding strategies for economically important orchids.

Research from Nature Portfolio

Studies of ndh gene evolution have shown that independent deletions and transfers of chloroplast-derived ndh fragments to the mitochondrial genome have occurred across orchid subfamilies, demonstrating the dynamic fate of photosynthetic apparatus genes. Shifts in IR/SSC junctions correlate with the presence or absence of ndhF, implicating this gene in boundary stability. In another focus, comparative plastome analyses of Dendrobium species identified ten highly variable loci that remain consistent even as sampling increases, providing a robust set of mutational hotspots for low-level phylogenetics and species identification. These findings underscore the utility of targeted regions for resolving relationships within a genus characterised by rapid diversification.

Chloroplast Genome Evolution in Orchidaceae publication trend

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

Technical terms

Chloroplast genome: The circular DNA molecule within chloroplasts that encodes genes for photosynthesis and gene expression.

Quadripartite structure: The four-part organisation of most chloroplast genomes, comprising two inverted repeats and two single-copy regions.

Inverted repeats (IRs): Identical sequences in reverse orientation that separate the large and small single-copy regions and contribute to genome stability.

Single-copy regions (LSC and SSC): Genomic segments flanked by inverted repeats; the LSC typically contains most genes, while the SSC is smaller and more variable.

ndh genes: A family of eleven chloroplast genes encoding subunits of the NAD(P)H dehydrogenase complex involved in cyclic electron flow.

Mutational hotspot: A genomic region exhibiting high sequence variability, useful as a molecular marker for phylogenetic and population studies.

References

1. Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species. International Journal of Molecular Sciences (2023).
2. Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes. BMC Plant Biology (2023).
3. Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences. BMC Plant Biology (2022).
4. Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots. Scientific Reports (2017).
5. Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries. PLOS ONE (2015).
6. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Scientific Reports (2015).
7. The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions. BMC Plant Biology (2021).
8. Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution. International Journal of Molecular Sciences (2018).
9. Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences. Frontiers in Plant Science (2020).