Ribes malvaceum is commonly known as Chaparral Currant. This pilot project aimed to create genomic resources for R. malvaceum for phylogenomic studies of secondary metabolite production. The Ribes sp. are of interest in this study due to production of bioactive compounds for human health. R. malvaceum is of interest due to its desirable climate resiliency traits. Based on known characteristics of closely related cultivated species Ribes nigrum and the best BLASTX results, we hypothesize that we will find transcriptomic evidence of similar secondary metabolites produced by R. malvaceum in the transcripts.
Ribes malvaceum tissue was collected on the Red Trail at Gold Creek Preserve, Angeles National Forest. Leaf and fruit tissue was snap frozen in the field and sent to BGI Americas for extraction, library preparation, and sequencing. The data pipeline for plant RNAseq consisted of QC, de novo assembly, BUSCO evaluation, quantification, and annotation. The shell script find_transcript_ids.sh was used to find lant transcripts with TPM>10 (Transcripts Per Million) and length>1000. The downstream analysis was performed in order to narrow down interesting secondary metabolite genes which had high length and high TPM. The BUSCO results showed that the transcriptome was 90.63% complete.
Delta (8)-fatty-acid desaturase sequences were closely related to Helianthus (70.43% similar), TPM=42.85, length= 2115. Transcripts closely matched Chalcone synthase from Humulus, with 90.69% similarity and length of 1506, and were elevated (TPM= 644.85). A transcript related to Flavonoid 3’-monooxygenase in Petunia was identified (77.57% similar), length 2075, TPM=132.70. Anthocyanidin reductase ((2S)-flavan-3-ol-forming) was highly similar to Vitis (84.57%), TPM=39.75, length=1249. Monothiol glutaredoxin was related to the sequence Arabidopsis (70.67% similar, TPM=49.77, effective length=3616). Transcripts related to 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2 were identified that were 87.69% similar to Vitis (TPM=231.54, effective length= 1029).
These results are a starting point for further investigation into the species’ resiliency and natural products.
