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.
