Identification and Analysis of Alternative Splicing Events in Scutellaria baicalensis Georgi with Different Stem Colors Based on Transcriptome Sequencing

Gao Yanxia; Wang Binbin; Xie Yan; Lu Yang; Sun Zhichao; Zhao Chunying; Wang Hui

doi:10.14083/j.issn.1001-4942.2026.02.002

Abstract：Alternative splicing(AS)is a common post-transcriptional regulatory mechanism that modu-lates gene expression and increases protein diversity.In field-grown Scutellaria baicalensis Georgi,stems typi-cally exhibit two colors,green and purple.Plant coloration is closely associated with anthocyanins,and AS regulates the biosynthesis of anthocyanins and other flavonoids.In this study,transcriptome sequencing(RNA-seq)was performed using epidermal and cortical tissues from green-stem and purple-stem S.baicalensis.A to-tal of 30 100 cDNA sequences and 3 241 novel transcripts were assembled,and five types of AS events were i-dentified,namely exon skipping(ES),intron retention(IR),alternative 3' splice site(A3'SS),alternative 5' splice site(A5'SS),and mutually exclusive exons(MXE).Using two quantification methods,junction counting(JC)and junctions and exons combined counting(JCEC),129 450 and 129 504 AS events were i-dentified respectively,and the number of differential AS events were 3 878 and 3 939,which were distributed in 2 052 and 2 097 differential genes,respectively.The number of up-regulated alternatively spliced isoforms was lower than that of down-regulated isoforms.Among different AS types,the number of genes showed a de-creasing trend as the number of alternatively spliced isoforms increased.GO annotation analysis indicated that the differentially alternatively spliced genes were mainly enriched in the pathways related to substance metabo-lism and chloroplast components.KEGG annotation analysis revealed these genes were primarily enriched in carbohydrate and amino acid metabolism pathways.A total of 62 differentially alternatively spliced genes relat-ed to anthocyanin biosynthesis were identified,including transcription factor genes of the MYB,bHLH and WD40 families,as well as structural genes involved in anthocyanin biosynthesis.The results of this study could provide a meaningful reference for elucidating the functions and regulatory roles of AS in the formation of dif-ferent stem colors in S.baicalensis.