Yixuan Rao

Ms. Yixuan Rao


Research Focus & Metrics

Academic Career Length

2Years (2025-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
26 September 2025 in Genes
Verified
Journal Article
Open access
PDF file
HMHui Ma
Hui Ma
YRYixuan Rao
Yixuan Rao
XLXiao yin Lu
Xiao yin Lu
NFNa Fang
Na Fang
YHYijia Huang
Yijia Huang
LGLei Gong
Lei Gong
Background: Plastid RNA editing is widespread in angiosperms yet remains underexplored in the medicinal non-model species Glycyrrhiza uralensis. This study aimed to (i) comprehensively identify plastid RNA editing sites in G. uralensis, and (ii) compare the detection performance of three library construction strategies: total RNA-seq, rRNA-depleted RNA-seq, and mRNA-seq. Methods: Leaf tissue was used from three wild-sampled individual plants. Plastomes were assembled with GetOrganelle v1.7.0 and annotated using PGA. Strand-specific RNA-seq libraries were mapped to sample-matched plastomes using HISAT2 v2.2.1. Variants were identified using REDItools v2.0 under uniform thresholds. Candidate sites were visually verified in IGV v2.12.3, and read origins were confirmed by BLAST v2.13.0+; artifacts were removed via strand-specific filtering. Results: After stringent filtering, 38 high-confidence RNA editing sites were identified across 19 genes. Total RNA seq performed the best, detecting 37/38 sites consistently, whereas rRNA-depleted libraries detected fewer genuine sites and produced numerous rRNA-linked, noncanonical, noncoding-strand-dominant artifacts. Despite very low rates of plastid mapping, mRNA seq recovered a large fraction of bona fide sites under stringent, strand-aware filtering. Conclusions: We establish a set of 38 high-confidence plastid RNA editing sites in G. uralensis and suggest potential adaptive implications of editing in ndh-related genes. Methodologically, total RNA-seq is recommended for identification using de novo RNA editing due to its high sensitivity and low false-positive rate; publicly available poly(A)-selected mRNA-seq datasets can be repurposed to reliably retrieve plastid RNA editing sites when stringent strand-specific filtering is applied.