De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (<i>Quercus agrifolia</i>)

De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (<i>Quercus agrifolia</i>)

Coast Live Oak (<i>Quercus agrifolia</i>) is a native keystone hardwood species of the California coastal and semi-arid forest environment. <i>Q. agrifolia</i> is threatened by pathogens such as the oomycete <i>Phytophthora ramorum</i>, which is known to cause Sud...

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Bibliographic Details
Main Authors: Savanah Senn, Ray A. Enke, Steven J. Carrell, Bradley Nations, Meika Best, Mathew Kostoglou, Karu Smith, Jieyao Yan, Jillian M. Ford, Les Vion, Gerald Presley
Format: Article
Language:English
Published: MDPI AG 2025-02-01
Series:Applied Microbiology
Subjects:
<i>Quercus</i>
fire ecology
RNAseq
plant–microbe interactions
microbial ecology
sequencing
Online Access:https://www.mdpi.com/2673-8007/5/1/24
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Summary:Coast Live Oak (<i>Quercus agrifolia</i>) is a native keystone hardwood species of the California coastal and semi-arid forest environment. <i>Q. agrifolia</i> is threatened by pathogens such as the oomycete <i>Phytophthora ramorum</i>, which is known to cause Sudden Oak Death in environments from Southern California to Oregon. This study considers oaks and their rootzone microbes recovering from moderate and low-intensity fires in rapid succession, compared to high- and low-intensity fires with a large time gap between them. cDNA libraries from nine oak leaf tissue samples were sequenced on DNBseq. Soil samples were sent out for shotgun metagenomics and for 16S community profiling. The de novo <i>Q. agrifolia</i> assembly yielded 521,817 transcripts with an average length of 805.2 bp. Among identified DEGs (differentially expressed genes) between the trail areas, several candidate genes were identified including shikimate dehydrogenase and myrcene synthase. The MegaBLAST results showed a high degree of similarity to WGS sequences from <i>Q. agrifolia</i> that had been previously annotated in other closely related <i>Quercus</i> species. There was a differential abundance of microbial genera associated with the different burn areas, including <i>Pedobacter</i>, <i>Filimonas</i>, <i>Cohnella</i>, and <i>Sorangium</i>. The data embody the first <i>Q. agrifolia</i> transcriptome that with further development could be used to screen oak seedlings for resistance; beneficial microbial populations have been identified that are associated with fire recovery under varied conditions.
ISSN:2673-8007

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