Transcriptomic profile of Arabidopsis thaliana treated with exogenous Riboflavin
Riboflavin, also known as vitamin B2, is crucial for cell function as it is the central component of FMN and FAD cofactors. These flavocoenzymes are essential for various cellular processes including the control of flavoproteins activity. Flavins are vital for growth and cellular metabolism of plants, supporting functions like photosynthesis, mitochondrial electron transport, and fatty acid oxidation. Further, previous studies have shown that exogenous application of riboflavin enhances plant defenses against abiotic and biotic stresses. In this study, to identify and implicate genes and signaling pathways involved in these processes, a holistic transcriptome analysis was conducted on Arabidopsis wild-type plants treated with Riboflavin and the mutant called “melin” which accumulates Riboflavin at exceptionally high levels. Overall design: Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer's instructions from six days-old Col-0 (wild-type) and fmn/fhy (mos) seedlings grown under standard conditions: 16 hours of light and 8 hours of darkness per day, with a light intensity of 100 µmol m–2 s–1. Additionally,  RNA was extracted from Col -0 (wild-type) (CR) seedlings treated with 0.6 mM Riboflavin for 8 hours during the dark cycle. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis. RNA-seq libraries were generated using the polyA Strand-Specific Transcriptome Library method of BGI  for DNBSEQ platform. Sequencing was performed on DNBSEQ platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample. Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using SOAPnuke (version 1.5.2) with parameters “-l 15 -q 0.2 -n 0.05" and the HISAT2 pipeline (version 2.0.4) with parameters “--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8".