Genome-wide identification and characterization of tissue-specific non-coding RNAs in black pepper (Piper nigrum L.)

Abstract

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are the two classes of non-coding RNAs (ncRNAs) present predominantly in plant cells and have various gene regulatory functions at pre- and post-transcriptional levels. Previously deemed as “junk”, these ncRNAs have now been reported to be an important player in gene expression regulation, especially in stress conditions in many plant species. Black pepper, scientifically known as Piper nigrum L., despite being one of the most economically important spice crops, lacks studies related to these ncRNAs. From a panel of 53 RNA-Seq datasets of black pepper from six tissues, namely, flower, fruit, leaf, panicle, root, and stem of six black pepper cultivars, covering eight BioProjects across four countries, we identified and characterized a total of 6406 lncRNAs. Further downstream analysis inferred that these lncRNAs regulated 781 black pepper genes/gene products via miRNA–lncRNA–mRNA network interactions, thus working as competitive endogenous RNAs (ceRNAs). The interactions may be various mechanisms like miRNA-mediated gene silencing or lncRNAs acting as endogenous target mimics (eTMs) of the miRNAs. A total of 35 lncRNAs were also identified to be potential precursors of 94 miRNAs after being acted upon by endonucleases like Drosha and Dicer. Tissue-wise transcriptome analysis revealed 4621 circRNAs. Further, miRNA–circRNA–mRNA network analysis showed 432 circRNAs combining with 619 miRNAs and competing for the binding sites on 744 mRNAs in different black pepper tissues. These findings can help researchers to get a better insight to the yield regulation and responses to stress in black pepper in endeavor of higher production and improved breeding programs in black pepper varieties.

Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Cyprinus carpio L.)

“…The investigation into tissue-specific circRNAs in common carp gave 22,854 circRNAs and GO analysis suggests that lncRNAs/circRNAs play a crucial role in various cellular processes, including transcriptional regulation, signaling pathways, and enzymatic reactions, which could have implications for various biological processes, including development, growth, directly involved in immunity, and disease ( Xiu et al, 2021 ). For identification of circRNAs on common carp, CIRI2 was used owing to its robustness and reliability as compared to other methods, based on numerous literature ( Gao et al, 2018 ; Chen et al, 2022 ; Kumar et al, 2023 ; Rbbani et al, 2023 ). In tilapia fish, ten and eleven circular RNAs were predicted to target miR-221 and miR-222, correspondingly.…”

Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard

“…chinensis), it was observed that lncRNAs and miRNAs regulate heat stress responses through pathways associated with plant hormones ( Wang et al, 2019 ). Using publicly available RNA-seq data, exploring lncRNAs and their regulatory networks in plants has become a feasible strategy ( Chen, Zhong & Qi, 2021 ; Kumar et al, 2023 ; Xie et al, 2023a ; Xie et al, 2023b ). For instance, under drought stress conditions, Chen et al (2021) identified a set of upregulated lncRNAs involved in regulating genes related to carbon fixation, chlorine metabolism, and fatty acid synthesis.…”

Comprehensive Analysis of Differentially Expressed lncRNAs in Papaver somniferum L.

“…The lncRNAs were distributed unevenly across the 11 opium poppy chromosomes, consistent with previous ndings (Guo et al 2018; Hong et al 2022).It is well known that lncRNAs show tissue-or developmental stage-speci c expression pro les(Budak et al 2020). Previous studies have shown that tissue-speci cally expressed lncRNAs often have speci c functions(Zhao et al 2020;Kumar et al 2023…”