This project established transcriptome and soil metagenomic resources for Trichostema lanatum. T. lanatum is a traditional Chumash medicinal plant in Lamiaceae used for rheumatism, commonly called wooly blue curls. The stunning flowers and leaves were collected from the Gold Creek Preserve, Angeles National Forest. What made these plants so resilient to abiotic and biotic stress?
In May 2022, snap-frozen plant tissue for RNA sequencing and soil for DNA sequencing were collected. The pipeline for plant RNAseq consisted of QC in SOAPnuke and MultiQC, de novo assembly in Trinity, BUSCO evaluation, quantification in salmon, and annotation with Trinotate. Metabarcoding was analyzed with DNA Subway Purple Line. Soil metagenomics were analyzed in Nephele using BioBakery, MicrobiomeDB, and STAMP.
The Trichostema lanatum transcriptome assembly was 91.1% complete according to BUSCO results. Plant isoforms with TPM > 10 and effective length > 1000 were chosen for a downstream analysis. Transcripts were annotated with the best Sprot BLASTX and BLASTP hits.
In the plant transcripts, there was a prevalence of functions related to primary defense mechanisms that would make the plant more resilient such as pectins, heat shock proteins, a stress response, RIPP-like disease resistance proteins, chitinase-like proteins; transcripts for anti-herbivory-related functions were also abundant, especially coumarates such as scopoletin analogs and glucoalkaloids like strictosinide. Shikimate O-hydroxycinnamoyltransferase was most closely related to Nicotiana (TPM = 132, length = 1816, 84.37% ID). Phenylalanine ammonia lyase (PAL) was annotated from Digitalis (TPM = 57.53, length = 2874, 91.02% similar). There was an elevated expression of Cadmium-related heavy metal resistance genes and heavy-metal-associated isoprenylated proteins.
In soil WGS results from the wooly blue curls’ rootzone, TPMs were above average for flavonoid and isoflavonoid biosynthesis and stilbene and isoquinoline alkaloid biosynthesis compared to other plant rootzones in the National Forest preserve studied. Abundances were similar for tropane, piperidine, and pyridine alkaloid and indole alkaloid production, and lower for indole diterpene alkaloid biosynthetic genes, compared to the other rootzones. There were also differences in taxonomic composition; there was a higher than average proportion of reads for unclassified bacteria and unclassified Actinomycetota sp. These results emphasize candidate genes related to phenylpropanoid production as potential actors adding to the resilience of Trichotestema lanatum against oxidative abiotic and biotic stress, both above ground and below ground.
Author Contributions
Conceptualization, S.S.; methodology, S.S. and S.J.C.; software, S.J.C.; formal analysis, S.S., S.J.C. and K.B.-K.; investigation, S.S., D.M., K.S., A.L.B., M.K. and L.V.; resources, S.S., G.P., B.N. and R.A.E.; data curation, J.H. and S.S.; writing—original draft preparation, S.S. and J.H.; visualization, S.S.; funding acquisition, B.N. and R.A.E. All authors have read and agreed to the published version of the manuscript.
Funding
This work was supported by training and resources from the National Science Foundation IUSE grant, NSF DUE-1821657 awarded to Bruce Nash and Ray Enke in part to support Community College faculty. This material is based upon work supported by the National Science Foundation under Grant Nos. DBI-0735191, DBI-1265383, and DBI-1743442 which supported iPlant Collaborative and DNA Subway development.
Institutional Review Board Statement
Not applicable.
Informed Consent Statement
Not applicable.
Data Availability Statement
Raw reads have been deposited on the NCBI Short read archive (SRA) repository. Soil metagenomic reads are available under PRJNA1064914: Gold Creek 2022 Soil Metagenomics on NCBI; RNAseq SRAs are available under BioProject PRJNA1046570: Gold Creek 2022 RNA sequencing. Metabarcoding data is available on DNA subway Public Project # 9586.
Acknowledgments
Thank you to the Gold Creek Committee, Los Angeles Community College District.
Conflicts of Interest
The authors declare no conflicts of interest.
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