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Identification and characterization of tissue- and stress-specific circular RNAs
(circRNAs) of tea to generate the largest tea circRNAs data repository
#MMPMID41131129
Rawal HC
; Pal RK
; Mondal TK
Sci Rep
2025[Oct]; 15
(1
): 36999
PMID41131129
show ga
Enormous RNA-seq data of tea (Camellia sinensis) is available at NCBI, yet only
3,174 circular RNAs (circRNAs) have been reported to date. This study establishes
a foundation for using public datasets to generate circRNA reservoirs. After
standardizing the pipeline using in-house RNA-seq data from Indian tea, 178
RNA-seq datasets of tea were downloaded from NCBI and used for the generation of
the largest tissue and stress-specific tea circRNAs repository (TCDB;
http://indianteagenome.in:8080/tcdb/ ), till date. A total of 3052 and 59,575
full-length circRNA isoforms were identified from Indian tea and downloaded
public datasets, respectively. Notably, only 10% of these shared homologies with
known plant circRNAs, indicating that 90% are novel. Since only 9.77% circRNAs
were shared between 25,651 and 39,750 circRNAs from stress- and tissue-related
RNA-seq data, respectively, mostly are either tissue- or stress-specific.
Annotation of parental genes of differentially expressed circRNAs (DECs)
highlighted their roles in important pathways, including phenylpropanoid
biosynthesis, aminoacyl-tRNA biosynthesis, and regulation of different
metabolisms. Although circRNA-miRNA interaction analysis favors the role of
circRNAs as miRNA sponges, with 17% of circRNAs having no miRNA interactions,
there could be other possible functions of circRNAs. While circRNA data generated
at this large scale could serve as foundation for in-depth studies on tea
circRNAs, the strategy of using available public RNA-seq data to detect circRNAs
and conduct further downstream analysis will aid in accelerating similar studies
in other species.
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