Identification and characterization of long non-coding RNA (lncRNA) in wild and semi-wild cucumbers

Abstract

Abstract Background The cucumber (Cucumis sativus) is a model species for genomic studies in vegetables due to its relatively small genome size. Long non-coding RNAs (lncRNAs) play crucial roles in plant growth, development, and stress responses. LncRNAs are less conserved among plant species and comparative genomic study of lncRNA in cucumbers can provide new insight about the evolution and function of cucumber lncRNAs. Results Here, full-length transcriptome sequencing was applied to identify high-confidence lncRNAs in wild (C. sativus var. hardwickii) and semi-wild (C. sativus var. xishuangbannanensis) cucumbers. A total of 1,598 lncRNAs were screened out, and these lncRNAs exhibit distinct characteristics, including fewer exons, shorter sequences, and lower GC content when compared with messenger RNAs (mRNAs). We observed a slight expansion of lncRNAs, such as lncRNA family 1, which could contain up to 21 members distributed across different chromosomes. These family members are typically derived from the same genomic region, likely as a result of alternative splicing. Differentially expressed lncRNAs (DELs) may cis-regulate the expression of nearby genes, and functional enrichment analysis indicated that the primary biological process involved was environmental adaptation. We predicted that eighteen lncRNAs could serve as microRNA (miRNA) precursors, generating 25 miRNAs, which subsequently target 1,628 protein-coding genes. Functional enrichment analysis revealed that these target genes were primarily enriched in epigenetic regulatory pathways, suggesting a complex feedback regulation involving epigenetic modifications and gene expression. The competing endogenous RNA (ceRNA) network analysis revealed that 31 lncRNAs interacted with 26 miRNAs and competed for 134 targeted protein-coding genes. MiR156 plays a crucial role in the ceRNA network, competing with CsLncRNA94 to target the 7 members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor gene family. We observed that CsLncRNA94 participates in the miR156-SPL module’s response to light and low temperature and acts as a negative regulator of cold tolerance in cucumber, as demonstrated through transient expression in cotyledons. Conclusions Full-length lncRNAs were identified in wild- and semi-wild cucumbers. The differential expression of lncRNAs between cucumbers with different domestication degree is likely for environmental adaptation particularly via lncRNA-miRNA pathway. CsLncRNA94 is a representative lncRNA that regulate miR156-SPL module in response to light and temperature stimuli. Clinical trial number Not applicable.

Keywords

• Cucumber
• LncRNA
• MiRNA
• CeRNA network
• SPLs