Spliced leader RNA trans-splicing discovered in copepods

Area of Science:

• Marine Biology
• Molecular Biology
• Genomics

Background:

• Copepods are abundant marine organisms crucial for food webs and carbon cycling.
• Understanding copepod gene expression is vital but currently limited.
• Spliced leader (SL) trans-splicing is a gene expression mechanism found in various organisms.

Purpose of the Study:

• To detect and characterize SL trans-splicing in calanoid copepods.
• To develop a tool for studying copepod transcriptomics.
• To identify molecular mechanisms of gene expression in copepods.

Main Methods:

• Examined nine wild-caught copepod species from Jiaozhou Bay, China.
• Determined spliced leader RNA (slRNA) size and structure using genomic analysis, 3'-RACE, and RNA blot analysis.
• Utilized a CopepodSL-based primer set for full-length cDNA enrichment and sequencing.

Main Results:

• Detected common 46-nt spliced leader (CopepodSL) in all nine species.
• Confirmed CopepodSL precursor RNA (slRNA) size (108–158 nt) and typical secondary structure.
• Characterized copepod transcripts and cataloged 79 eukaryotic cytoplasmic ribosomal proteins (cRPs) for one species.
• Demonstrated CopepodSL as a sensitive and specific tool for individual and population-level copepod transcriptomics.

Conclusions:

• SL trans-splicing is present in natural populations of calanoid copepods.
• CopepodSL is an effective tool for comprehensive copepod transcriptomic and metatranscriptomic analysis.
• This discovery advances the study of gene expression in ecologically important marine invertebrates.