Chloroplast Genome Analysis in Quercus Species

Chloroplast genomes in Quercus have been extensively characterised over the past decade, revealing a conserved quadripartite circular structure composed of a large single‐copy (LSC) region, a small single‐copy (SSC) region and two inverted repeats (IRs). Genome sizes typically range from 160 000 to 162 000 base pairs, with stable gene content and order across sections such as Cyclobalanopsis, Cerris and Ilex. Comparative genomics has identified mutational hotspots (for example, trnK-rps16, psbC-trnS, rbcL-accD and ycf1) and simple sequence repeats (SSRs) that serve as valuable molecular markers for species discrimination and phylogeographic studies. Selection analyses have detected positively selected genes (notably ycf2, petA and rpoC1) linked to environmental adaptation. High‐throughput sequencing and comprehensive phylogenetic reconstructions have refined our understanding of oak diversification during the Miocene and delineated infrageneric relationships, informing taxonomy, conservation strategies for vulnerable taxa and investigations into historical biogeography under climate change.

Research from Nature Portfolio

Recent studies have sequenced and assembled the complete chloroplast genomes of four species in section Cyclobalanopsis using Illumina pair‐end technology, revealing genome sizes between 160 715 and 160 842 base pairs. Conserved GC content and IR boundaries were observed alongside six highly variable regions (including rpoC1, clpP and ycf1) proposed as molecular markers. Signals of positive selection in petA and ycf2 genes suggest adaptation to ecological pressures. Maximum‐likelihood and Bayesian phylogenetic trees corroborate the morphological grouping of compound trichome base species into distinct clades, though some infrageneric groups remain unresolved due to low node support, indicating the need for expanded sampling and complementary nuclear data.

Chloroplast Genome Analysis in Quercus Species publication trend

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

Technical terms

Chloroplast genome (cp genome): The circular DNA molecule within chloroplasts encoding genes essential for photosynthesis and other plastid functions.

Inverted repeats (IR): Two identical sequence segments in opposite orientation that separate the single‐copy regions in the chloroplast genome.

Large single‐copy region (LSC) and small single‐copy region (SSC): Genomic regions between inverted repeats, differing in length and gene content.

Simple sequence repeats (SSRs): Short tandemly repeated DNA motifs used as molecular markers for population genetics and phylogeography.

Phylogenetic analysis: Computational methods to reconstruct evolutionary relationships among species using genomic data.

Positive selection: Evolutionary process favouring advantageous genetic variants, detectable by elevated non-synonymous substitution rates.

Hotspots: Genome regions with elevated nucleotide variability, often exploited for marker development.

References

1. Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis. Frontiers in Plant Science (2024).
2. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Scientific Reports (2023).
3. Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species. Genes (2022).
4. Comprehensive Analysis of Codon Usage in Quercus Chloroplast Genome and Focus on psbA Gene. Genes (2022).