Differential expression of genes in Quercus agrifolia from different fire history areas in the Angeles National Forest

Our study established transcriptomic and soil metagenomic resources for Quercus agrifolia (leaf). Q. agrifolia is a hardwood that may live for centuries.

Samples were collected from three fire history areas in Gold Creek Preserve, Angeles National Forest. Low, medium, and high intensity burn areas are referred to as the Blue, Green, and Red Trails. In our previous work, we showed taxonomic differences in fungi and bacteria in the three different fire areas. The current study sought associations between plant gene expression and microbial functions.

During May 2022, snap frozen plant tissue samples for RNA sequencing and soil samples for metagenome sequencing were collected. The bioinformatics for plant RNAseq was QC in SOAPnuke and MultiQC, Trinity de novo assembly, BUSCO evaluation, salmon quantification, and annotation with Trinotate. Metabarcoding analysis used DNA Subway Purple Line. Soil metagenomic analysis was carried out in Nephele BioBakery, MicrobiomeDB, and STAMP.

For oaks, the transcriptome was 96.17% complete according to the BUSCO assessment. Three trees were sampled from each of 3 burn areas which allowed for contrasts in DEseq2 based on the tree location. There was evidence of differential gene expression related to the isoprenoid pathway, freezing resistance, drought response, and pathogen defense. However, there was some evidence of heterogeneity of gene expression within the clusters, for the top 25 differentially expressed genes.

In WGS results, there was not strong evidence of functional differences associating the soil microbiome of Q. agrifolia with plant secondary metabolite production. However, there were taxonomic & alpha diversity differences associated with different areas of the preserve, each having different fire histories. Further studies should focus on microbes associated with plant tissues and their potential association with plant secondary metabolite production. For example, further experiments should use woody tissues.