Artemisia californica draft leaf and flower transcriptome and soil WGS resources

Secondary metabolite production in Artemisia has been studied for its anti-parasitic, anti-tumor, and anti-inflammatory actions. Artemisia californica is a drought resilient plant with medicinal value used traditionally as a topical for severe pain relief; flavonoids, stilbenes, sesquiterpene lactones, and terpenes are main therapeutic components.

We aimed to create novel genomic resources, including a leaf & flower transcriptome and soil WGS metagenomics from the A. californica rootzone. Snap frozen plant tissues and rhizosphere soil were collected from the field and sent to BGIA for extraction, library preparation, and sequencing. Following QC, de novo assembly and quantification, transcripts were annotated with the best SPROT BLASTX and BLASTP hits. The completeness of the assemblies was assessed using BUSCO. Transcripts with TPM>10 and length>1000 were examined for evidence of candidate genes related to production of the expected bioactive compounds.

Assembly summary statistics were computed. There were 212,818 total sequences with a total length of 2.07*10^8. The average sequence length was 908; the length ranged between 193-13,630. L50 value was 41,357, N50 was 1,591, and N80 was 647. The Artemisia californica transcriptome was 91.4% complete. In the transcripts, there was evidence of sesquiterpene production, sesquiterpene lactones, and flavonoids. Beta-caryophyllene synthase was related to Artemisia, however with low similarity (62.70% ID, TPM= 14.86, length=2889). Multiple sesquiterpenoids and triterpenoids appeared to be elevated. Chalcone synthase transcripts were 96.23% similar to Australasian lineages of Asteraceae.

There was evidence of a distinct rootzone microbial community. Geodermatophilus from Actinomycetes was well-represented. The Biobakery metagenomics output indicated that there are differences in taxonomy in soil samples from different plant species, although there were few differences in function.

Future studies should focus on Nanopore sequencing of plant RNA and mining for novel bacterial species in the Artemisia rootzone using WGS data. Further studies should include biochemical analysis to confirm genomic findings.