Comparative Study of Leaf Cell DNA from Four Oak Tree Species

Jenn Hoskins
11th June, 2024

Comparative Study of Leaf Cell DNA from Four Oak Tree Species

Image Source: Natural Science News, 2024

Key Findings

  • Researchers from China West Normal University sequenced and analyzed the chloroplast genomes of ten Quercus section Cyclobalanopsis species
  • The study found that the chloroplast genomes of these species are highly conserved in structure and size, with no rearrangements or inversions detected
  • Phylogenetic analysis revealed that Quercus hui was the first to diverge, while Quercus disciformis and Quercus blackei are closely related, aiding in species classification and evolutionary studies
The Quercus L. species, commonly found in the broad-leaved evergreen forests of tropical and subtropical East Asia, are economically significant due to their use as firewood, furniture, and street trees. However, identifying these species and understanding their relationships have been challenging. In a recent study conducted by China West Normal University, researchers sequenced and assembled the chloroplast genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui) and retrieved six published chloroplast genome sequences of other Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia) for comparative genomics and phylogenetic analyses[1]. The chloroplast (cp.) genome is an essential component for studying plant genetics and evolution as it is highly conserved and maternally inherited. Chloroplast genomes typically exhibit a quadripartite structure, consisting of a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeats (IRs). This study confirmed that the cp. genomes of the newly sequenced Quercus species exhibit this typical tetrad structure, with genome lengths ranging from 160,787 bp to 160,806 bp. One of the key findings was the detection of 469 simple sequence repeats (SSRs), which are short, repetitive DNA sequences. Among these, A/T base repeats were the most common, providing useful markers for genetic studies and species identification. Notably, no rearrangements or inversions were detected within the chloroplast genomes, indicating a high degree of structural conservation. The study also identified genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2. These genes serve as potential reference loci for molecular identification within the Cyclobalanopsis section, aiding in the accurate classification and differentiation of Quercus species. Phylogenetic analysis revealed that the ten Cyclobalanopsis species were grouped into sister taxa, with Quercus hui being the first to diverge from the evolutionary branch and Quercus disciformis being the most closely related to Quercus blackei. These findings are consistent with previous studies that have highlighted the evolutionary significance of Quercus species in East Asian evergreen broadleaved forests[2][3]. For instance, the comprehensive phylogeny of Quercus section Cyclobalanopsis using RAD-seq demonstrated the monophyly of the section and its biogeographical history tied to climatic changes and tectonic activities[2]. Additionally, the complete chloroplast genome of Quercus chungii, another member of the Cyclobalanopsis section, was previously assembled, providing insights into its genetic structure and evolutionary relationships with other Quercus species[3]. This new study expands on these findings by offering a broader comparative analysis of multiple Cyclobalanopsis species, enhancing our understanding of their genetic diversity and evolutionary history. The development of a new visualization tool specifically designed for chloroplast genomes has also facilitated the analysis of genetic architecture in Quercus species[4]. This tool allows researchers to depict the genetic structure of chloroplast genomes accurately, providing deeper insights into their evolutionary relationships and aiding in the identification of species. In conclusion, the study by China West Normal University presents significant advancements in the understanding of Quercus section Cyclobalanopsis species. By sequencing and analyzing the chloroplast genomes of ten species, the researchers have provided valuable genetic markers, confirmed structural conservation, and elucidated phylogenetic relationships. These findings form a crucial foundation for future taxonomic and phylogenetic studies, contributing to the conservation and utilization of these economically and ecologically important species.

GeneticsPlant ScienceEvolution

References

Main Study

1) Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis

Published 10th June, 2024

https://doi.org/10.1186/s12863-024-01232-y

Related Studies

2) Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia.

https://doi.org/10.1016/j.ympev.2017.11.003

3) The complete chloroplast genome sequence of Quercus chungii (Fagaceae).

https://doi.org/10.1080/23802359.2021.1931505

4) IRscope: an online program to visualize the junction sites of chloroplast genomes.

https://doi.org/10.1093/bioinformatics/bty220


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